Relevant bibliographies by topics / Branched RNA

Academic literature on the topic 'Branched RNA'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Branched RNA"

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Edmonds, Mary. "Branched RNA." BioEssays 6, no. 5 (May 1987): 212–16. http://dx.doi.org/10.1002/bies.950060505.

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Grøtli, Morten, Ramon Eritja, and Brian Sproat. "Solid-phase synthesis of branched RNA and branched DNA/RNA chimeras." Tetrahedron 53, no. 33 (August 1997): 11317–46. http://dx.doi.org/10.1016/s0040-4020(97)00731-x.

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Nakashima, Yuko, Hiroshi Abe, Naoko Abe, Kyoko Aikawa, and Yoshihiro Ito. "Branched RNA nanostructures for RNA interference." Chemical Communications 47, no. 29 (2011): 8367. http://dx.doi.org/10.1039/c1cc11780g.

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Aviñó, Anna, Sandra M. Ocampo, José Carlos Perales, and Ramon Eritja. "Branched RNA: A New Architecture for RNA Interference." Journal of Nucleic Acids 2011 (2011): 1–7. http://dx.doi.org/10.4061/2011/586935.

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Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.
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Kierzek, Ryszard, David W. Kopp, Mary Edmonds, and Marvin H. Caruthers. "Chemical synthesis of branched RNA." Nucleic Acids Research 14, no. 12 (1986): 4751–64. http://dx.doi.org/10.1093/nar/14.12.4751.

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Lilley, David M. J. "Folding of branched RNA species." Biopolymers 48, no. 2-3 (1998): 101–12. http://dx.doi.org/10.1002/(sici)1097-0282(1998)48:2<101::aid-bip2>3.0.co;2-7.

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Wang, Yangming, and Scott K. Silverman. "Characterization of Deoxyribozymes That Synthesize Branched RNA†." Biochemistry 42, no. 51 (December 2003): 15252–63. http://dx.doi.org/10.1021/bi0355847.

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Wang, Yangming, and Scott K. Silverman. "Deoxyribozymes That Synthesize Branched and Lariat RNA." Journal of the American Chemical Society 125, no. 23 (June 2003): 6880–81. http://dx.doi.org/10.1021/ja035150z.

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Damha, Masad J., and Kelvin K. Ogilvie. "Synthesis and spectroscopic analysis of branched RNA fragments: messenger RNA splicing intermediates." Journal of Organic Chemistry 53, no. 16 (August 1988): 3710–22. http://dx.doi.org/10.1021/jo00251a010.

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Lönnberg, Tuomas A. "Can Phosphate-Branched RNA Persist under Physiological Conditions?" ChemBioChem 13, no. 18 (November 26, 2012): 2690–700. http://dx.doi.org/10.1002/cbic.201200629.

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Dissertations / Theses on the topic "Branched RNA"

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Bryson, David Irby. "Targeting RNA Structures with Multivalent Branched Peptide Libraries." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77327.

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RNA is essential for the transfer of genetic information, as the central dogma of biology dictates. The role of RNA, however, is not limited to serving as an information shuttle between DNA and fully functional protein. Indeed, RNA has experienced a surge of interest in the field of chemical biology for its other critical roles in biology including those in control of transcription, translation, splicing, genetic replication, and catalysis. RNA has proven to be a difficult and complex target for the design of small molecular ligands because of its structural heterogeneity and conformational flexibility. Yet, the highly folded tertiary structures of these oligomers present unique scaffolds which designed ligands should be able to selectively target. To that end, two branched peptide libraries ranging in size from 4,096–46,656 unique sequences were screened for their ability to bind HIV-1 related RNA structures, the transactivation response element (TAR) and the Rev response element (RRE). In addition to discovering a mid-nanomolar branched peptide ligand for TAR, the first branched boronic acid peptide library designed to target RNA was screened for binding to RRE. Each of these efforts resulted in the identification of selective binders to their respective RNA targets, and the unnatural branching of these compounds was demonstrated to provide a multivalent binding interaction with the RNA. Furthermore, these compounds were shown to be cell permeable and displayed little to no cytotoxicity in HeLa and A2780 cells.
Ph. D.
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Ghafouri, Rouzbeh. "From annealed branched polymers with excluded volume effects to viral RNA condensation." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1782063231&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Zhang, Wenyu. "Targeting HIV-1 RNAs with Medium Sized Branched Peptides Featuring Boron and Acridine-Branched Peptide Library Design, Synthesis, High-Throughput Screening and Validation." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/56731.

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RNAs have gained significant attention in recent years because they can fold into well-defined secondary or tertiary structures. These three dimensional architectures provide interfaces for specific RNA-RNA or RNA-protein interactions that are essential for biological processes in a living system. These discoveries greatly increased interest in RNA as a potential drug target for the treatment of diseases. Two of the most studied RNA based regulatory systems are HIV-1 trans-activating response element (TAR)/Tat replication pathway and Rev response element (RRE)/Rev export pathway. To efficiently target TAR and RRE RNA, we designed and synthesized three generations of branched peptide libraries that resulted in medium sized molecules. The first generation of BPs were discovered from screening a one-bead one-compound library (4,096 compounds) against HIV-1 TAR RNA. One peptide FL4 displayed a binding affinity of 600 nM to TAR RNA, which is tighter than its native protein counterpart, Tat. Biophysical characterization of these BP demonstrated that "branches" in BPs impart multivalency, and they are cell permeable and non-toxic. The second generation peptides were discovered from an on-bead high-throughput screening of a 3.3.4 branched peptide boronic acids (BPBAs) library that bind selectively to the tertiary structure of RRE IIB. The library comprised of 46,656 unique sequences. We demonstrate that our highest affinity BPBA (BPBA1) selectively binds RRE IIB in the presence of competitor tRNAs as well as against six RRE IIB structural variants. Further, we show that the boronic acid moieties afford a novel binding mode towards RNA that is tunable; their Lewis acidity has critical effects on binding affinity. In addition, biophysical characterizations provide evidence that "branching" in these peptides is a key structural motif for multivalent interactions with the target RNA. Finally, RNA footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB. BPBA1 is cell permeable and non-toxic. In the next generation of branched peptides, a 3.3.4 branched peptide library composed of 4,096 unique sequences that featured boronic acid and acridine moieties was designed. We chose acridine as the amino acid side chain due to its potential for π-stacking interaction that provides high binding affinity to RNA target. The library was screened against HIV-1 RRE IIB RNA. Fifteen peptides were sequenced and four contained acridine alone and/or in conjunction with boronic acid moieties displayed dissociation constants lower than 100 nM. The ribonuclease protection assays of A7, a sequence that contains both boronic acid and acridine residues, showed a similar protection pattern compared to previous peptide BPBA1, suggesting that the 3.3.4 branched peptides shared similar structural elements and contacted comparable regions of the RRE IIB RNA. The results from this research indicated that "branching" in peptides imparts multivalent interactions to the RNA, and that functional groups such as boronic acid and acridine are key structural features for efficient binding and selectivity for the folded RNA target. We demonstrated that the branched peptides are cell permeable and non-toxic.
Ph. D.
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Wynn, Jessica Elaine. "Functionalizing Branched Peptides with Unnatural Amino Acids Toward Targeting HIV-1 RRE RNA and Microbials." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/82227.

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The interaction of the protein Rev with Rev Response Element (RRE) RNA is critical to the HIV-1 life cycle as this complex is required for the export of singly-spliced and unspliced mRNAs from the nucleus to the cytoplasm. Disruption of this interaction is considered to be a powerful strategy towards the development of HIV-1 therapeutics. Therefore, we have developed several branched peptide libraries containing unnatural amino acids to target the high-affinity binding site of RRE RNA (RRE IIB), with the idea that branching in peptides can provide multivalent contacts with folded RNA structures and boost binding affinity and selectivity for the target. Unnatural amino acids were incorporated into the library design to encourage non-canonical interactions with the RNA and to improve proteolytic stability. The on-bead high-throughput screening of our first branched peptide library (46,656 sequences) against HIV-1 RRE RNA generated hit peptides with binding affinities in the low micromolar range. We demonstrated that branching in the peptide is required for efficient binding and selectivity towards the RNA, and that the peptides bind a large surface area of RRE IIB. Introduction of boronic acids into branched peptides boosted selectivity of the peptides for RRE IIB, and proved to be a novel and tunable mode of binding towards RNA. Additionally, we revealed that these branched peptide boronic acids (BPBAs) were cell permeable and non-toxic. One BPBA (BPBA3) bound RRE IIB selectively and was able to inhibit HIV-1 replication in vitro, revealing enzymatic cleavage of the RNA upon binding. A second generation BPBA library that introduced acridinyl lysine as an intercalator (4,096 sequences) was screened against RRE IIB. Several hit compounds bound in the low nanomolar regime, and a significant number of compounds inhibited HIV-1 replication in vitro. These BPBAs were also found to severely inhibit the microbial growth of bacteria and fungus, with MICs as low as 1 µg/mL against Staphylococcus aureus, Candida albicans, and Escherichia coli. These compounds were also found to significantly inhibit biofilm formation and growth, and were non-hemolytic. High-throughput screening of a third generation BPBA library containing all unnatural amino acids (46,656 sequences) revealed several hits that bound RRE IIB RNA in the nanomolar range. Sequence motifs present in the hit peptides suggested that the location and composition of amino acids within the branched peptide structure were important for recognizing the RNA target. In particular, lead compounds 2C5 and 4B3 demonstrated selectivity towards RRE, and footprinting experiments combined with SHAPE experiments revealed different interactions of the peptides with the RNA Toxicity assays revealed no impact on cell viability for the majority of hit sequences tested up to 100 µM, and several compounds also demonstrated inhibition of HIV-1 replication.
Ph. D.
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Sabatino, David. "Expanding the size and shape of nucleic acids : studies on branched and heptose based nucleic acids." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103291.

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The generation of synthetic oligonucleotides is dependent on an efficient solid-phase synthesis methodology. This thesis evaluates the 2'-O -levulinyl (Lv) and 2'-O-monomethoxytrityl (MMT) ribonucleosides, as possible synthons for RNA and branched RNA synthesis. A key feature of this RNA and bRNA synthesis procedure is their removal while still attached to the solid support and under conditions that prevent isomerization or cleavage of the nascent strands. For the first time, the stability of 3'-5'-internucleotide phosphate triesters (and diesters) adjacent to a ribose 2'-hydroxyl group was determined on a solid support. These studies are not only relevant to the proper assembly of branched and linear RNA species, but also to the stability of an unusual branched RNA species ("RNA X") proposed to form during the pre-mRNA splicing reactions in vitro. These studies are also important to the development of large quantities of native and chemically modified short interfering RNA (siRNA) for animal and human studies.
The 2'-O-Lv and 2'-O-MMT ribonucleoside monomers served as building blocks for the assembly of a series of branched nucleic acid species (bRNA, bDNA, msDNA and hyperbranched or "dendritic" DNA/RNA) with discrete length, base composition and structure. These structures were synthesized via an iterative divergent-growth strategy, which facilitates the regioselective branching, deblocking and chain lengthening steps from a branchpoint core. These structures served as useful materials (bio-probes) as demonstrated by the biological studies performed with E. coli RNaseH and the yeast lariat RNA debranching enzyme (yDBr1). These studies not only led to the identification of novel branched nucleic acid inhibitors of yDBR1 and RNase H, but also provided new insights about the substrate specificity of these important enzymes.
This thesis also describes the synthesis of a new nucleic acid form, the so-called "oxepane nucleic acids" (ONAs), in which the pentofuranose ring of DNA and RNA was replaced with a 7-membered heptose sugar ring. ONA were found to be much more resistant towards nuclease degradation than natural DNA, an important feature if these analogues are to be used in biological media. Furthermore, ONAs exhibited cross-pairing with complementary RNA and were found to elicit E. coli RNaseH mediated degradation of the RNA strand. These finding are significant because oligonucleotide-directed RNase H degradation of the target RNA is a key determinant for the gene-specific inhibitory potency of antisense oligonucleotides. When comparing the rates of RNase H-mediated degradation induced by 5 (furanose), 6 (2'-ene-pyranose) and 7 (oxepane) membered ring oligonucleotides, the following trend was observed: DNA > 2'-ene-pyranose NA > ONA. The implications of these results are discussed in the context of our current understanding of the catalytic mechanism of the enzyme, particularly with regard to the required flexibility of the oligonucleotide strands that bind to the RNA target. Hence, ONAs are useful tools for biological studies and provide new insights into the structure/function of natural and alternative genetic systems.
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Mourani, Rawan. "Synthesis, characterization and biological properties of branched RNA fragments containing chiral (Rþ and Sþ) 2',5'-phosphorothioate linkages." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=29458.

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A method to synthesize a diastereomeric mixture of 2',5 '-phophorothioate A(psG) dimers in solution was developed. The sulfurizing reagent "EDITH" allowed for the synthesis of the diastereomeric mixture of dimers with minimal formation of oxidized side products. The separation of the two isomers was carried out using silica gel flash chromatography to afford the stereoisomerically pure Rp and S p dimers. The orthogonal solution-phase coupling of the individual dimers to the appropriately protected monomers allowed for the creation of the corresponding branched trimers bearing vicinal 2',5'-phophorothioate and 3',5'-phosphodiester linkages.
Conversely, a convergent solid-phase strategy applicable to the synthesis of branched oligonucleotides was employed to construct a symmetrical branched phosphodiester trimer, A(pG)pG, using an adenosine bisphosphoramidite synthon. This compound served as a positive control substrate, relative to both the Sp and Rp-phophorothioate V-trimers, in the investigation of the stereochemical requirements of the yeast debranching enzyme (yDBR) at the 2',5'-phosphodiester linkage. (Abstract shortened by UMI.)
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Issa, Mohamed Mahmoud. "Linear and Branched Chitosan Oligomers as Delivery Systems for pDNA and siRNA In Vitro and In Vivo." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7376.

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Javadi-Zarnaghi, Fatemeh [Verfasser], Claudia [Akademischer Betreuer] Höbartner, Reinhard [Akademischer Betreuer] Lührmann, Kai [Akademischer Betreuer] Tittmann, Marina [Akademischer Betreuer] Rodnina, Detlef [Akademischer Betreuer] Doenecke, and Jörg [Akademischer Betreuer] Stülke. "Functional characterization and application of 2',5'- branched RNA forming deoxyribozymes using lanthanides as cofactors / Fatemeh Javadi-Zarnaghi. Gutachter: Claudia Höbartner ; Reinhard Lührmann ; Kai Tittmann ; Marina Rodnina ; Detlef Doenecke ; Jörg Stülke. Betreuer: Claudia Höbartner." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2013. http://d-nb.info/1049580737/34.

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Javadi-Zarnaghi, Fatemeh Verfasser], Claudia [Akademischer Betreuer] Höbartner, Reinhard [Akademischer Betreuer] Lührmann, Kai [Akademischer Betreuer] Tittmann, Marina [Akademischer Betreuer] Rodnina, Detlef [Akademischer Betreuer] [Doenecke, and Jörg [Akademischer Betreuer] Stülke. "Functional characterization and application of 2',5'- branched RNA forming deoxyribozymes using lanthanides as cofactors / Fatemeh Javadi-Zarnaghi. Gutachter: Claudia Höbartner ; Reinhard Lührmann ; Kai Tittmann ; Marina Rodnina ; Detlef Doenecke ; Jörg Stülke. Betreuer: Claudia Höbartner." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2013. http://d-nb.info/1049580737/34.

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Gould, Genevieve Michelle. "Identification of novel branch points reveals insights into RNA processing." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/101293.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
Pre-mRNA splicing is a ubiquitous process necessary for the production of functional eukaryotic mRNAs. The branch point (BP) sequence is one of three key nucleotide sequences required for pre-mRNA splicing, however, in metazoa it has been less comprehensively studied than the 5' splice site (5'SS) and 3' splice site (3'SS) due to the relative difficulty of identifying each sequence element. 5'SS and 3'SS are readily identified by aligning spliced cDNAs, ESTs, or RNA-Seq reads to the genome, while lower throughput techniques such as primer extension are usually required to map BPs, with some exceptions. To understand how the BP affects splicing outcomes, we developed an experimental method to locate BPs on a genome-wide scale. Applying our method to Saccharomyces cerevisiae (S. cerevisiae), one of the only eukaryotes for which most BPs are known, allowed us to assess the sensitivity and specificity of our method. We enriched for RNA lariats by isolating RNA from debranching enzyme null yeast and purified circular RNAs (including lariats) from linear RNAs using a 2D PAGE gel. This was followed by a custom library preparation protocol that produced insert ends that identified the BP and 5'SS of individual lariats. Using this method, we located known BPs and discovered a substantial number of novel BPs both in annotated introns and other genomic regions. We attempted to verify these novel introns using RNA-seq and Lariat-seq and surprisingly observed considerable amounts of alternative splicing (AS) in S. cerevisiae beyond the previously known stress-regulated intron retention events and handful of alterative splice sites. Additionally, we observed several introns with 2 BPs and one intron with 3 BPs. In the LSM2 transcript, we showed alternative BP usage was associated with alternative splice site usage, where one of the mRNA isoforms contains a premature termination codon and leads to nonsense-mediated mRNA decay of the transcript. This suggests AS may control gene expression levels in yeast as is known to be the case in metazoans. Preliminary application of our method to Drosophila melanogaster showed recursive splicing, a phenomenon known only to occur in introns larger than 10Kb, to occur in a 383nt intron.
by Genevieve Michelle Gould.
Ph. D.
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Books on the topic "Branched RNA"

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Zi ran liao fa bai ke: Jia ting Zhong yi DIY bai ke = Nature therapy hundred branches. Taizhong Shi: Chen xing chu ban you xian gong si, 2008.

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Lykhin, P. A. Strategii︠a︡ i prot︠s︡essy osvoenii︠a︡ georesursov: Materialy nauchnoĭ sessii Gornogo instituta UrO RAN po rezulʹtatam NIR v 2003 godu, 19-23 apreli︠a︡ 2004 g., Permʹ = Strategy and processes of mastering of georesource : materials of scientific session of Mining Institute of Ural Branch of the Russian Academy of Sciences, 19-23 April 2004, Perm. Permʹ: Gornyĭ in-t Uralʹskogo otdelenii︠a︡ RAN, 2004.

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Costandi, Shrif, Youssef Saweris, Michael Kot, and Nagy Mekhail. Thoracic Facet Nerve Block: Fluoroscopy. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199908004.003.0015.

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The benefit of intra-articular local anaesthetic and steroid injections for the diagnosis and treatment of facet joint pain is controversial. Thoracic facet medial branch blocks are mainly used to confirm the diagnosis of thoracic facet arthropathy. Anatomic variability is blamed for failed treatments. Conventionally, thermal radiofrequency (RF) has been used to denervate thoracic facet joints. Cooled radiofrequency ablation (c-RFA) of the thoracic medial branch is emerging as a novel promising technique that provides relatively larger lesions that could compensate for the anatomic variation of these branches and improve outcomes. The most feared complication of RF procedures in the thoracic region is pneumothorax, which may manifest as shortness of breath or pain with inspiration. Using proper technique for placement of the needles under fluoroscopic guidance renders the risk of this complication almost negligible.
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Kindler, Peter, and Jan Lieder, eds. European Corporate Law. Nomos Verlagsgesellschaft mbH & Co. KG, 2021. http://dx.doi.org/10.5771/9783845279909.

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The purpose of the European directives on corporate law is to enable businesses to be set up anywhere in the EU, to provide protection for shareholders and other parties with a particular interest in companies, to make business more efficient and competitive, and to encourage businesses based in different EU countries to cooperate with each other. The new Commentary on Corporate Law provides an in-depth expert analysis of all legal issues concerning the setting up and several other main issues covered by EU corporate law. With a view to offering recommendation for practical applications, the book covers, article-by-article, the following European directives: Directive (EU) 2017/1132 relating to certain aspects of company law, including - Safeguards (former Safeguards Directive, 2009/101/EC) - Disclosure requirements (former Directive concerning disclosure requirements in respect of branches, 89/666/EEC) - Public limited liability companies (former Directive concerning the formation of public limited liability companies, 2012/30/EU) - Mergers and Division (former Directives concerning of public limited liability companies, 2005/56/EC and 2011/35/EU) - Cross Border Mergers (former Directive 82/891/EEC) Directive concerning single-member private limited liability companies (2009/102/EC) Directive on Takeover Bids (2004/25/EC) Shareholder Rights Directive (2007/36/EC) Directive on the annual financial statements (2013/43 EU) and on statutory audits of annual accounts (2006/43/EC) <b>The Authors</b>: RA Dr. Klaus Bader, Dr. Martin Bialluch, RA Dr. Andreas Börner, RA Dr. Jan P. Brosius, LL.M. (King’s College London), RAin Larissa Furtwengler, David Günther, RA Dr. Simon Jobst, Maître en droit, Prof. Dr. Dr. h.c. Peter Kindler, RA Karsten Kühnle, RA Dr. Michael Lamsa, RA Prof. Dr. Dieter Leuering, Prof. Dr. Jan Lieder, LL.M. (Harvard), RAin Dr. Silja Maul, Prof. Dr. Hanno Merkt, LL.M. (Chicago), RA Dr. Tobias De Raet, Prof. Dr. Alexander Schall, M.Jur. (Oxon). This publication is part of IEBL-series – Commentaries on International and European Business Law: www.iebl.info
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Hilliard, Christopher. It Is Not My Verdict. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198799658.003.0012.

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Scurrilous letters continued to circulate after Edith Swan’s acquittal. The authorities moved again nearly two years later. The DPP sought the help of the General Post Office’s Investigative Branch. They ran a sting operation using stamps specially marked with invisible ink. Swan was caught and charged again. Her second trial was another media event, and Travers Humphreys, again appearing for the prosecution, felt obliged to remind the jury ‘that they were not living in the pages of a sensational novel, but . . . were dealing with facts in real life’. Swan appeared before Mr Justice Avory again, who summed up in her favour, but the jury found her guilty and she went to prison for a year.
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Kirchman, David L. Predation and protists. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0009.

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Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.
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Book chapters on the topic "Branched RNA"

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Soh, Kah Teong, and Paul K. Wallace. "RNA Flow Cytometry Using the Branched DNA Technique." In Flow Cytometry Protocols, 49–77. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7346-0_4.

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Zhu, Xiaoli, Chang Feng, and Genxi Li. "Nicking Enzyme-Assisted Branched-Chain RCA Reaction for Cascade DNA Amplification." In Rolling Circle Amplification (RCA), 49–56. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-42226-8_5.

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Greenbaum, Nancy L. "Role of a conserved pseudouridine in U2 snRNA on the structural and electrostatic features of the spliceosomal pre-mRNA branch site." In Fine-Tuning of RNA Functions by Modification and Editing, 205–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/b106846.

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"Branched RNA." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 233. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_2025.

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INOUYE, SUMIKO, TEIICHI FURUICHI, ANIL DHUNDALE, and MASAYORI INOUYE. "Stable Branched RNA Covalently Linked to the 5′ End of a Single-Stranded DNA of Myxobacteria." In Molecular Biology of RNA, 271–84. Elsevier, 1987. http://dx.doi.org/10.1016/b978-0-12-372483-0.50020-x.

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David Reilly, J., John C. Wallace, Randa F. Melhem, David W. Kopp, and Mary Edmonds. "[15] Isolation and characterization of branched oligonucleotides from RNA." In Methods in Enzymology, 177–91. Elsevier, 1989. http://dx.doi.org/10.1016/0076-6879(89)80101-6.

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Lilley, David M. J. "The Structure and Folding of Branched RNA Analyzed by Fluorescence Resonance Energy Transfer." In Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B, 159–87. Elsevier, 2009. http://dx.doi.org/10.1016/s0076-6879(09)69008-x.

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Lilley, David M. J. "[23] Analysis of global conformation of branched RNA species using electrophoresis and fluorescence." In Methods in Enzymology, 368–93. Elsevier, 2000. http://dx.doi.org/10.1016/s0076-6879(00)17025-9.

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Sharma, Dolly, Shailendra Singh, and Trilok Chand. "RNA Interference Therapeutics and Human Diseases." In Encyclopedia of Information Science and Technology, Fourth Edition, 477–90. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-2255-3.ch042.

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Defective protein synthesis leads to diseases. If protein synthesis can be controlled, disease causing molecules can be tailored in some way. This is the perception behind RNA interference. RNA interference (RNAi) Therapeutics is branch of medicine which deals with the treatment of diseases while controlling the gene expression at RNA level. The motive of this chapter is to discover the state- of-art of RNAi Therapeutics, to explore various techniques used by RNAi Therapeutics to fight from diseases and discuss the future prospects of it.
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Sharma, Dolly, Shailendra Singh, and Trilok Chand. "RNA Interference Therapeutics and Human Diseases." In Advanced Methodologies and Technologies in Medicine and Healthcare, 69–83. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7489-7.ch006.

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Defective protein synthesis leads to diseases. If protein synthesis can be controlled, disease causing molecules can be tailored in some way. This is the perception behind RNA interference. RNA interference (RNAi) therapeutics is branch of medicine which deals with the treatment of diseases while controlling the gene expression at RNA level. The motive of this chapter is to discover the state-of-the-art of RNAi therapeutics, to explore various techniques used by RNAi therapeutics to fight from diseases, and discuss the future prospects of it.
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Conference papers on the topic "Branched RNA"

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Asiruwa, John J., Aaron M. Propst, and Stephen P. Gent. "Hemodynamics Study of Different Take-Off Angles of the Left Coronary Artery." In 2017 Design of Medical Devices Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/dmd2017-3389.

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Coronary arteries are located on the surface of the heart and supply oxygenated blood to the myocardium and other components of the heart. The two coronary arteries located above the aortic arch are the Left Coronary Artery (LCA) and Right Coronary Artery (RCA). The LCA branches into the Left Anterior Descending (LAD) and the Left Circumflex (LCx) while the RCA branches into the Right Marginal Artery (RMA) and Post Descending Artery (PDA). The coronary arteries are likened to a complex tube-like structure, and the motion of the heart cause changes in pressure, which allows proper blood circulation during the systolic and diastolic phases [1]. Since it is essential to understand the physiological and hemodynamical behavior of the heart and coronary arteries, numerous studies have been conducted at different artery locations in the heart. Most of the research has focused on the branches between the LAD and LCx, with little or no attention directed towards the take-off angle the LCA makes with the aortic root. Although it has been reported that certain take-off angles of left main (LM) can be considered anomalous, findings have documented that such take off angles can make the artery prone to atherosclerosis and sudanophilia diseases [2]. Computational Fluid Dynamics (CFD) has in recent years been used to solve a wide variety of fluid flow challenges, and can be used for this study. The goal of this study is to use CFD techniques to study the hemodynamics of the different take-off angles of the left coronary artery from the aortic root. This will help identify areas in the left coronary artery that could be prone to atherosclerosis buildup.
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Myers, Jerry G., M. Ojha, K. Wayne Johnston, and C. Ross Ethier. "Branch Flow Effects in the Human Right Coronary Artery Trunk." In ASME 2000 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2000. http://dx.doi.org/10.1115/imece2000-2614.

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Abstract Formation of atherosclerotic plaque in the human right coronary artery (RCA) has, in part, been linked to local hemodynamic factors (Ojha et al., 2000). Thus, there is considerable motivation to accurately characterize hemodynamic patterns in the RCA. Patient-specific geometric characteristics, such as curvature and arterial calibre, have been shown to significantly affect velocity and wall shear stress (WSS) patterns within the RCA trunk (Myers et al., 2000). However it is unclear how flow into arterial branches influences these hemodynamic patterns. In investigating this factor, we computed velocity and WSS distributions in a realistic model of a human right coronary artery (RCA) that included four branches.
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Blazewicz, Jacek, Marek Figlerowicz, and Agnieszka Rybarczyk. "Branch and bound algorithm for nonenzymatic RNA degradation." In 2008 1st International Conference on Information Technology (IT 2008). IEEE, 2008. http://dx.doi.org/10.1109/inftech.2008.4621679.

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Reyes, Christopher, and Dumitru I. Caruntu. "Voltage Response for Parametrically Actuated MEMS Cantilever Beam Using Homotopy Analysis Method and Method of Multiple Scales." In ASME 2018 Dynamic Systems and Control Conference. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/dscc2018-9012.

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The purpose of this paper is to investigate the nonlinear dynamics governing the behavior of electrostatically actuated micro electro mechanical systems (MEMS) cantilever undergoing parametric resonance. The MEMS consists of a cantilever parallel to a ground plate. The beam is actuated via an A/C voltage with excitation frequency near first natural frequency of the cantilever. The model includes damping, electrostatic, and Casimir (or van der Waals) forces. The electrostatic force is modeled to include the fringe effect. The amplitude-voltage response of the parametric resonance and the effects of varying the magnitudes of the fringe, Casimir (or Van der Waals), and damping forces along with varying the detuning parameter are reported. The response is obtained using two different methods, namely the method of multiple scales (MMS), and the homotopy analysis method (HAM). In this study approximations up to a 2nd order HAM are used. HAM is a deformation technique that begins with an initial guess and continuously deforms it to the exact answer. For the 1st Order HAM, a softening effect is reported. The 1st Order HAM matches the MMS results in low amplitude and begins to soften and deviate away from the MMS solution in higher amplitudes. For the 2nd Order HAM deformation the softening effect is slightly more pronounced with a slightly lower prediction of the maximum deflection of the cantilever tip. For the 2nd order deformation solution the stable branch of the amplitude-voltage response obtained by the HAM shifts leftward from the MMS solution with the unstable branches between the two methods continue to agree in low amplitudes and deviate in high amplitudes. As a remark, the higher order HAM solutions are obtained symbolically with the software Mathematica and numerically ran with the software Matlab.
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Bemova, V. D., Т. V. Yakusheva, and М. Sh Asfandiyarova. "ECOLOGICAL AND GEOGRAPHICAL STUDYING OF PEANUT SAMPLES BY ECONOMICALLY VALUABLE TRAITS." In 11-я Всероссийская конференция молодых учёных и специалистов «Актуальные вопросы биологии, селекции, технологии возделывания и переработки сельскохозяйственных культур». V.S. Pustovoit All-Russian Research Institute of Oil Crops, 2021. http://dx.doi.org/10.25230/conf11-2021-24-28.

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Peanut seeds are valuable nut-bearing raw materials widely used in food and confectionary industries. Unfortunately, industrial sowings of peanut in Russia are absent. Thereat it is necessary to look for new material for breeding. Conduction of ecological and geographical trials allowed finding the most productive and large-seeded samples from the VIR’s collection. The trial results also showed the significant impact of reproduction place on economically valuable traits. Thus, ripening rate is higher in Cis-caspian Agrarian Federal Scientific Center of the Russian Academy of Sciences (PAFNTs RAN) compared to the Kuban experimental station – a branch of N.I. Vavilov All-Russian Institute of Plant Genetic Resources (KOS VIR).
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Zanini, Luiz G. K., Aldomar P. S. Silva, Felipe V. de Almeida, Fátima L. S. N. Marques, and Anna H. R. Costa. "Convolutional architectures with LSTM and TCN to embolism classification: exploring dependency between data." In Encontro Nacional de Inteligência Artificial e Computacional. Sociedade Brasileira de Computação - SBC, 2022. http://dx.doi.org/10.5753/eniac.2022.227585.

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Pulmonary Embolism is an affection caused by obstruction of the pulmonary artery or one of its branches. This condition imposes a high mortality incidence, in the United States approximately 100.000 deaths per year. Computed Tomography Pulmonary Angiography is a radiologic modality and an essential technology for diagnosing this disease, providing a series of axial images. We trained two Convolutional Neural Networks (Efficient Net B0 and Resnet 3D 18) in the RSNA-STR Computed Tomography Pulmonary Angiography Dataset to identify this affection. After training these Convolutional Neural Networks, we added a new layer to the architecture by exploring the dependency between the images along the exam using Long Short-Term Memory or Temporal Convolutional Networks. With the models trained and tested, we compared these different approaches using different metrics. As a result, the Temporal Convolutional Network approach with Resnet 3D 18 improved significantly compared to the results found in the other methods. The main contribution of this work was to observe how different combinations of architectures can help classify Computed Tomography Pulmonary Angiography.
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Zhu, Xixi, Naihua Wang, and Xiangyu Chi. "Numerical Study on Gas Entrainment by Vortex in T-Junctions." In 2022 29th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/icone29-91855.

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Abstract Gas entrainment by free surface vortices in the Residual Heat Removal System (RHRS) would affect the safety of the reactor at the mid-loop operation for nuclear power plants. Thus, it is important to estimate the occurrence of this entrainment accurately. In this work, two-phase Computational Fluid Dynamics (CFD) simulations of a T-junction are performed. In the T-junction, the diameters of the branch/main pipes are 40/142.5 mm, and the lengths of the branch/main pipes are 3Db/6Dm. The Volume of Fluid (VOF) method and RNG k-ε model are employed in this simulation to get a clear gas-liquid interface. And, several cases of different flow rates at the mid-loop operation are studied. The simulation results could show the phenomena of free surface waves, the free surface vortex formation and evolution, gas entrainment by free surface vortex. At a low flow rate, the free surface in the main pipe is relatively stable with no wave, there is no occurrence of vortex core or vortex in the T-junction. With the flow rate increasing, the free surface in the main pipe begins to fluctuate, vortex core occurs below the free surface. It evolves downstream and disappears in the main pipe soon. The free surface waves in the main pipe become more intense when the flow rate continues to increase, and the free surface vortex begins to entrain air into the branch as the vortex core evolving downstream in the main pipe in a very short time. The phenomena of numerical simulation show a good agreement with experimental results. In this paper, physical fields are also analyzed to determine the effect and mechanism of the gas entrainment by free surface vortices.
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Samad, A., and S. J. Garrett. "The Convective Instability of Boundary-Layer Flows Over Rotating Spheroids." In ASME 2009 Fluids Engineering Division Summer Meeting. ASMEDC, 2009. http://dx.doi.org/10.1115/fedsm2009-78484.

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The continuous development of spinning projectiles and other industrial applications has led to the need to understand the laminar boundary-layer flow and subsequent onset of transition over the general family of rotating spheroids. We begin by finding the laminar boundary-layer flow over a general spheroid. In particular, we distinguish between prolate and oblate spheroids and use an appropriate spheroidal coordinate system in each case. The laminar-flow equations are established for each family of spheroid rotating in otherwise still fluid. An eccentricity parameter e is used to distinguish particular bodies within the oblate or prolate families. In each case, setting e = 0 reduces the equations to those already established by Howarth [2] and Banks [4] for the rotating sphere. In this preliminary study the laminar-flow equations at each latitude are solved by extending the original series solutions due to Howarth and Banks for the rotating sphere. The laminar flows obtained are consistent with established results for the rotating sphere as e tends to zero, and tend to the von Ka´rma´n [5] solution for the rotating disk as the latitude is reduced close to the nose. Analyses of the convective instability are performed on the rotating prolate family. These extend the linear analyses previously published by Malik, Lingwood and Garrett & Peake [6–10] on related geometries. An investigation into the relative importance of type I (crossflow) and type II (streamline curvature) modes is also presented. At low latitudes increasing eccentricity has negligible effects on the stability characteristics of the flow. However as the latitude increases, eccentricity is seen to lower the upper (type I) branch of the neutral curve, reducing the region of instability.
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Ross, Malcolm K., and Don Hovdebo. "Environmental Assessment Perspective of Decommissioning and Long-Term Management of Uranium Mine Tailings in Saskatchewan, Canada." In ASME 2001 8th International Conference on Radioactive Waste Management and Environmental Remediation. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/icem2001-1256.

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Abstract Uranium was initially mined in Canada as a strategic mineral, primarily for export to the United States. Currently, uranium is produced for the global energy market and Saskatchewan is the sole producing province in Canada. Uranium development in Saskatchewan dates from 1953 and in 2000 accounted for 31% of global mine production. In the 1990’s the Saskatchewan Government Environmental Assessment Branch reviewed a new generation of uranium mines with large reserves and extremely high average grades. Technically, the development of these mines has required the development of innovative technologies to manage the environmental and occupational health and safety issues associated with the mining of high-grade uranium ores. While the development of these innovative technologies posed a challenge to science and engineering, the potential environmental impacts and level of public concern associated with the development of the high grade uranium deposits equally challenged the ability of the Province of Saskatchewan’s environmental assessment process to evaluate the acceptability of the proposed mines. During the assessment process a major technical, and public, issue was the decommissioning and long-term management of uranium tailings containing high levels of radionuclide and metal contaminants. While technically decommissioning and reclamation are phases of mining that are considered at the end of mine life, scrutiny of these issues during the assessment process contributed significantly to the public and technical acceptability of the proposed mine developments. The design, construction, operation, decommissioning and reclamation of uranium tailings management facilities for the proposed high-grade mines were subject to critical analysis during the technical and public review phases of the environmental assessment processes. Advances in tailings management design, incorporating innovative in-pit disposal methods capable of isolating decommissioned tailings from local groundwater regimes, presented a technical solution to concerns about long-term tailings containment after decommissioning. Public awareness and acceptance of the proposed mine developments was enhanced by the creation of an independent, public inquiry which ran concurrently with the existing federal and provincial assessment processes. The public inquiry was a critical factor, providing an independent forum where the technical acceptability of the proposed long-term tailings management methodologies was discussed. In retrospect the development of the new mines reflects the successful application of an assessment and review process in that the projects met the tests of technical and public acceptability in a process that was seen to be fair, timely, rigorous and public.
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Reports on the topic "Branched RNA"

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Salas, R. G. The Effects of Age, Educational Level and Branch Membership upon the Attitudes of Male, RAN Officers. Part 3. Older Officers. Fort Belvoir, VA: Defense Technical Information Center, June 1990. http://dx.doi.org/10.21236/ada228790.

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Flaishman, Moshe, Herb Aldwinckle, Shulamit Manulis, and Mickael Malnoy. Efficient screening of antibacterial genes by juvenile phase free technology for developing resistance to fire blight in pear and apple trees. United States Department of Agriculture, December 2008. http://dx.doi.org/10.32747/2008.7613881.bard.

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Objectives: The original objectives of this project were to: Produce juvenile-free pear and apple plants and examine their sensitivity to E. amylovora; Design novel vectors, for antibacterial proteins and promoters expression, combined with the antisense TFL1 gene, and transformation of Spadona pear in Israel and Galaxy apple in USA. The original objectives were revised from the development of novel vectors with antibacterial proteins combined with the TFL-1 due to the inefficiency of alternative markes initially evaluated in pear, phoshomannose-isomerase and 2-deoxyglucose-6-phosphate phosphatase and the lack of development of double selection system. The objectives of project were revised to focus primarily on the development additional juvenile free systems by the use of another pear variety and manipulation of the FT gene under the control of several promoters. Based on the results creation of fire blight resistance pear variety was developed by the use of the juvenile free transgenic plant. Background: Young tree seedlings are unable to initiate reproductive organs and require a long period of shoot maturation, known as juvenile phase. In pear, juvenile period can last 5-7 years and it causes a major delay in breeding programs. We isolated the TFL1 gene from Spadona pear (PcTFL1-1) and produced transgenic ‘Spadona’ trees silencing the PcTFL1 gene using a RNAi approach. Transgenic tissue culture ‘Spadona’ pear flowered in vitro. As expected, the expression of the endogenous PcTFL1 was suppressed in the transgenic line that showed precocious flowering. Transgenic plants were successfully rooted in the greenhouse and most of the plants flowered after only 4-8 months, whereas the non-transformed control plants have flowered only after 5-6 years of development. Major achievements: Prior to flower induction, transgenic TFL1-RNAi ‘Spadona’ plants developed a few branches and leaves. Flower production in the small trees suppressed the development of the vegetative branches, thus resulting in compact flowering trees. Flowering was initiated in terminal buds, as described for the Arabidopsis tfl1 mutant. Propagation of the transgenic TFL1-RNAi ‘Spadona’ was performed by bud grafting on 'Betulifolia' rootstock and resulted in compact flowering trees. The transgenic flowering grafted plants were grown in the greenhouse under a long photoperiod for one year, and flowered continuously. Pollination of the transgenic flowers with ‘Costia‘ pear pollen generated fruits of regular shape with fertile F1 seeds. The F1 transgenic seedling grown in the greenhouse formed shoots and produced terminal flowers only five months after germination. In addition, grafted F1 transgenic buds flower and fruit continuously, generating hybrid fruits with regular shape, color and taste. Several pear varieties were pollinated with the transgenic TFL1-RNAi ‘Spadona’ pollen including `Herald Harw` that was reported to have resistance to fire blight diseases. The F-1 hybrid seedlings currently grow in our greenhouse. We conclude that the juvenile-free transgenic ‘Spadona’ pear enables the development of a fast breeding method in pear that will enable us to generate a resistance pear to fire blight. Implications: The research supported by this grant has demonstrated the use of transgenic juvenile free technology in pear. The use of the juvenile free technology for enhancement of conventional breeding in fruit tree will serve to enhance fast breeding systems in pear and another fruit trees.
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Carpita, Nicholas C., Ruth Ben-Arie, and Amnon Lers. Pectin Cross-Linking Dynamics and Wall Softening during Fruit Ripening. United States Department of Agriculture, July 2002. http://dx.doi.org/10.32747/2002.7585197.bard.

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Our study was designed to elucidate the chemical determinants of pectin cross-linking in developing fruits of apple and peach and to evaluate the role of breakage cross-linkages in swelling, softening, and cell separation during the ripening. Peaches cell walls soften and swell considerably during the ripening, whereas apples fruit cells maintain wall firmness but cells separate during late stages of ripening. We used a "double-reduction" technique to show that levels of non-methyl esters of polyuronic acid molecules were constant during the development and ripening and decreased only in overripe fruit. In peach, methyl and non-methyl esters increased during the development and decreased markedly during the ripening. Non-methyl ester linkages in both fruit decreased accompanied fruit softening. The identity of the second component of the linkage and its definitive role in the fruit softening remain elusive. In preliminary examination of isolated apples cell walls, we found that phenolic compounds accumulate early in wall development but decrease markedly during ripening. Quantitative texture analysis was used to correlate with changes to wall chemistry from the fresh-picked ripe stage to the stage during storage when the cell separation occurs. Cell wall composition is similar in all cultivars, with arabinose as the principal neutral sugar. Extensive de-branching of these highly branched arabinans pre-stages softening and cell-cell separation during over-ripening of apple. The longer 5-arabinans remain attached to the major pectic polymer rhamnogalacturonan I (RG I) backbone. The degree of RG I branching, as judged from the ratios of 2-Rha:2,4-Rha, also decreases, specially after an extensive arabinan de-branching. Loss of the 4-Rham linkages correlated strongly with the softening of the fruit. Loss of the monomer or polymer linked to the RG I produce directly or indirectly the softening of the fruit. This result will help to understand the fruit softening and to have better control of the textural changes in fruit during the ripening and especially during the storage. 'Wooliness', an undesirable mealy texture that is induced during chilling of some peach cultivars, greatly reduces the fruit storage possibilities. In order to examine the hypothesis that the basis for this disorder is related to abnormality in the cell wall softening process we have carried out a comparative analysis using the resistant cultivar, Sunsnow, and a sensitive one, Hermosa. We investigated the activity of several pectin- and glycan-modifying enzymes and the expression of their genes during ripening, chilling, and subsequent shelf-life. The changes in carbohydrate status and in methyl vs. non-methyl uronate ester levels in the walls of these cultivars were examined as well to provide a basis for comparison of the relevant gene expression that may impact appearance of the wooly character. The activities of the specific polygalacturonase (PGase) and a CMC-cellulase activities are significantly elevated in walls of peaches that have become wooly. Cellulase activities correlated well with increased level of the transcript, but differential expression of PGase did not correspond with the observed pattern of mRNA accumulation. When expression of ethylene biosynthesis related genes was followed no significant differences in ACC synthase gene expression was observed in the wooly fruit while the normal activation of the ACC oxidase was partially repressed in the Hermosa wooly fruits. Normal ripening-related loss of the uronic acid-rich polymers was stalled in the wooly Hermosa inconsistent with the observed elevation in a specific PGase activity but consistent with PG gene expression. In general, analysis of the level of total esterification, degree of methyl esterification and level of non-methyl esters did not reveal any major alterations between the different fruit varieties or between normal and abnormal ripening. Some decrease in the level of uronic acids methyl esterification was observed for both Hermosa and Sunsnow undergoing ripening following storage at low temperature but not in fruits ripening after harvest. Our results support a role for imbalanced cell wall degradation as a basis for the chilling disorder. While these results do not support a role for the imbalance between PG and pectin methyl esterase (PME) activities as the basis for the disorder they suggest a possible role for imbalance between cellulose and other cell wall polymer degradation during the softening process.
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Eyal, Yoram, Gloria Moore, and Efraim Lewinsohn. Study and Manipulation of the Flavanoid Biosynthetic Pathway in Citrus for Flavor Engineering and Seedless Fruit. United States Department of Agriculture, October 2003. http://dx.doi.org/10.32747/2003.7570547.bard.

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The proposal was aimed to identify and functionally characterize key genes/enzymes in the citrus flavanone neohesperidoside biosynthetic pathway and to use them as tools for metabolic engineering to decrease bitterness levels in grapefruit. The proposed section on fruit seediness was dropped as suggested by the reviewers of the proposal. Citrus flavor and aroma is composed of complex combinations of soluble and volatile compounds. The former includes mainly sugars, acids and flavanones, a subgroup of flavonoids that includes bitter compounds responsible for the bitter flavor of grapefruit and pummelo. Bitter species contain mostly bitter flavanone neohesperidosides, while non-bitter species contain mostly tasteless flavanone rutinosides. Both flavanone versions are diglycosides consisting of a rhamnose-glucose oligosaccharide a-linked at position 7 to the flavanone skeleton. However, in the bitter neohesperidosides the rhamnose is attached at position 2 of the glucose moiety, while in the tasteless rutinosides the rhamnose is attached at position 6 of the glucose moiety. Thus, the position of the rhamnose moiety, determined by the specificity of the last enzymes in the pathway- rhamnosyltransferase (1,2 or 1,6 specificity), is the determinant of the bitter flavor. Flavanones, like all flavonoids are synthesized via one of the branches of the phenylpropanoid pathway; the first committed step is catalyzed by the enzyme Chalcone synthase (CHS) followed by Chalcone isomerase (CHI). During the course of the work a key gene/enzyme in the biosynthesis of the bitter flavanones, a 1,2 rhamnosyltransferase (1,2RT), was functionally characterized using a transgenic cell-culture biotransformation system, confirming that this gene is a prime candidate for metabolic engineering of the pathway. This is the first direct functional evidence for the activity of a plant recombinant rhamnosyltransferase, the first confirmed rhamnosyltransferase gene with 1,2 specificity and the second confirmed rhamnosyltransferase gene altogether in plants. Additional genes of the flavanone pathway that were isolated during this work and are potential tools for metabolic engineering include (I) A putative 1,6 rhamnosyltransferase (1,6RT) from oranges, that is presumed to catalyze the biosynthesis of the tasteless flavanones. This gene is a prime candidate for use in future metabolic engineering for decreased bitterness and is currently being functionally characterized using the biotransformation system developed for characterizing rhamnosyltransferases. (2) A putative 7-0-glucosyltransferase presumed to catalyze the first glycosylation step of the flavanone aglycones. Silencing of gene expression in grapefruit was attempted using three genes: (1) The "upstream" flavonoid biosynthesis genes CHS and CHI, by antisense and co-suppression; and (2) The "downstream" 1,2R T, by an RNAi approach. CHS and CHI silencing resulted in some plants with a dramatically decreased level of the bitter flavanone neohesperidoside naringin in leaves. We have yet to study the long-term effect of silencing these genes on tree physiology, and on the actual bitterness of fruit. The effect of 1,2RT silencing on naringin content in grapefruit has yet to be examined, but a slow growth phenotype for these plants was noted. We speculate that silencing of the final glycosylation step of the flavanones delays their evacuation to the vacuole, resulting in accumulation of flavanones in the cytoplasm, causing inhibitory effects on plant growth. This speculation is yet to be established at the product level. Future metabolic engineering experiments are planned with 1,6RT following functional characterization.
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Staff - Social Functions - RBA Branches - London Office, 8 Old Jewry - Visitors attending a dinner given during Governor HC Coombs' visit - 24 May 1962. Reserve Bank of Australia, March 2021. http://dx.doi.org/10.47688/rba_archives_pn-002833.

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Staff - Social functions - RBA Branches - London Office, 8 Old Jewry - Visitors attending a dinner given during Governor HC Coombs' visit - 24 May 1962. Reserve Bank of Australia, March 2021. http://dx.doi.org/10.47688/rba_archives_pn-002777.

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