Sample records for evolved orthogonal ribosome

  1. Orthogonally Evolved AI to Improve Difficulty Adjustment in Video Games

    DEFF Research Database (Denmark)

    Hintze, Arend; Olson, Randal; Lehman, Joel Anthony


    (i.e. agents subject to fewer generations of evolution) make for easier opponents, while highly-evolved agents are more challenging to overcome. In this publication we test a new approach for difficulty adjustment in games: orthogonally evolved AI, where the player receives support from collaborating...... opponents. Furthermore, human interaction can modulate (and be informed by) the performance and behavior of collaborating agents. In this way, orthogonally evolved AI both facilitates smoother difficulty adjustment and enables new game experiences....

  2. Detection and Quantification of Ribosome Inhibition by Aminoglycoside Antibiotics in Living Bacteria Using an Orthogonal Ribosome-Controlled Fluorescent Reporter. (United States)

    Huang, Shijie; Zhu, Xuechen; Melançon, Charles E


    The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome-controlled green fluorescent protein (GFP) reporter that produce fluorescent signal when the orthogonal ribosome is inhibited. As a proof of concept, we demonstrate that these strains, when coexpressing homogeneous populations of aminoglycoside resistant ribosomes, act as sensitive and quantitative detectors of ribosome inhibition by a set of 12 structurally diverse aminoglycoside antibiotics. We suggest that this strategy can be extended to quantifying ribosome inhibition by other drug classes.

  3. Orthogonally Evolved AI to Improve Difficulty Adjustment in Video Games

    DEFF Research Database (Denmark)

    Hintze, Arend; Olson, Randal; Lehman, Joel Anthony


    (i.e. agents subject to fewer generations of evolution) make for easier opponents, while highly-evolved agents are more challenging to overcome. In this publication we test a new approach for difficulty adjustment in games: orthogonally evolved AI, where the player receives support from collaborating...... agents that are co-evolved with opponent agents (where collaborators and opponents have orthogonal incentives). The advantage is that game difficulty can be adjusted more granularly by manipulating two independent axes: by having more or less adept collaborators, and by having more or less adept...... opponents. Furthermore, human interaction can modulate (and be informed by) the performance and behavior of collaborating agents. In this way, orthogonally evolved AI both facilitates smoother difficulty adjustment and enables new game experiences....

  4. ONMCGP: Orthogonal Neighbourhood Mutation Cartesian Genetic Programming for Evolvable Hardware (United States)

    I, Fuchuan N.; I, Yuanxiang L.; E, Peng K.


    Evolvable Hardware is facing the problems of scalability and stalling effect. This paper proposed a novel Orthogonal Neighbourhood Mutation (ONM) operator in Cartesian genetic programming (CGP), to reduce the stalling effect in CGP and improve the efficiency of the algorithms.The method incorporates with Differential Evolution strategy. Demonstrated by experiments on benchmark, the proposed Orthogonal Neighbourhood Search can jump out of Local optima, reduce the stalling effect in CGP and the algorithm convergence faster.

  5. Large facilities and the evolving ribosome, the cellular machine for genetic-code translation. (United States)

    Yonath, Ada


    Well-focused X-ray beams, generated by advanced synchrotron radiation facilities, yielded high-resolution diffraction data from crystals of ribosomes, the cellular nano-machines that translate the genetic code into proteins. These structures revealed the decoding mechanism, localized the mRNA path and the positions of the tRNA molecules in the ribosome and illuminated the interactions of the ribosome with initiation, release and recycling factors. They also showed that the ribosome is a ribozyme whose active site is situated within a universal symmetrical region that is embedded in the otherwise asymmetric ribosome structure. As this highly conserved region provides the machinery required for peptide bond formation and for ribosome polymerase activity, it may be the remnant of the proto-ribosome, a dimeric pre-biotic machine that formed peptide bonds and non-coded polypeptide chains. Synchrotron radiation also enabled the determination of structures of complexes of ribosomes with antibiotics targeting them, which revealed the principles allowing for their clinical use, revealed resistance mechanisms and showed the bases for discriminating pathogens from hosts, hence providing valuable structural information for antibiotics improvement.


    CERN Document Server

    Deutz, André; Schütze, Oliver; Legrand, Pierrick; Tantar, Emilia; Tantar, Alexandru-Adrian


    This book comprises nine selected works on numerical and computational methods for solving multiobjective optimization, game theory, and machine learning problems. It provides extended versions of selected papers from various fields of science such as computer science, mathematics and engineering that were presented at EVOLVE 2013 held in July 2013 at Leiden University in the Netherlands. The internationally peer-reviewed papers include original work on important topics in both theory and applications, such as the role of diversity in optimization, statistical approaches to combinatorial optimization, computational game theory, and cell mapping techniques for numerical landscape exploration. Applications focus on aspects including robustness, handling multiple objectives, and complex search spaces in engineering design and computational biology.

  7. An evolved ribosome-inactivating protein targets and kills human melanoma cells in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Green David E


    Full Text Available Abstract Background Few treatment options exist for patients with metastatic melanoma, resulting in poor prognosis. One standard treatment, dacarbazine (DTIC, shows low response rates ranging from 15 to 25 percent with an 8-month median survival time. The development of targeted therapeutics with novel mechanisms of action may improve patient outcome. Ribosome-inactivating proteins (RIPs such as Shiga-like Toxin 1 (SLT-1 represent powerful scaffolds for developing selective anticancer agents. Here we report the discovery and properties of a single chain ribosome-inactivating protein (scRIP derived from the cytotoxic A subunit of SLT-1 (SLT-1A, harboring the 7-amino acid peptide insertion IYSNKLM (termed SLT-1AIYSNKLM allowing the toxin variant to selectively target and kill human melanoma cells. Results SLT-1AIYSNKLM was able to kill 7 of 8 human melanoma cell lines. This scRIP binds to 518-A2 human melanoma cells with a dissociation constant of 18 nM, resulting in the blockage of protein synthesis and apoptosis in such cells. Biodistribution and imaging studies of radiolabeled SLT-1AIYSNKLM administered intravenously into SCID mice bearing a human melanoma xenograft indicate that SLT-1AIYSNKLM readily accumulates at the tumor site as opposed to non-target tissues. Furthermore, the co-administration of SLT-1AIYSNKLM with DTIC resulted in tumor regression and greatly increased survival in this mouse xenograft model in comparison to DTIC or SLT-1AIYSNKLM treatment alone (115 day median survival versus 46 and 47 days respectively; P values IYSNKLM is stable in serum and its intravenous administration resulted in modest immune responses following repeated injections in CD1 mice. Conclusions These results demonstrate that the evolution of a scRIP template can lead to the discovery of novel cancer cell-targeted compounds and in the case of SLT-1AIYSNKLM can specifically kill human melanoma cells in vitro and in vivo.

  8. Orthogonal polynomials

    CERN Document Server

    Freud, Géza


    Orthogonal Polynomials contains an up-to-date survey of the general theory of orthogonal polynomials. It deals with the problem of polynomials and reveals that the sequence of these polynomials forms an orthogonal system with respect to a non-negative m-distribution defined on the real numerical axis. Comprised of five chapters, the book begins with the fundamental properties of orthogonal polynomials. After discussing the momentum problem, it then explains the quadrature procedure, the convergence theory, and G. Szegő's theory. This book is useful for those who intend to use it as referenc

  9. Orthogonal polynomials

    CERN Document Server

    Szegő, G


    The general theory of orthogonal polynomials was developed in the late 19th century from a study of continued fractions by P. L. Chebyshev, even though special cases were introduced earlier by Legendre, Hermite, Jacobi, Laguerre, and Chebyshev himself. It was further developed by A. A. Markov, T. J. Stieltjes, and many other mathematicians. The book by Szegő, originally published in 1939, is the first monograph devoted to the theory of orthogonal polynomials and its applications in many areas, including analysis, differential equations, probability and mathematical physics. Even after all the

  10. Structural insights into ribosome translocation. (United States)

    Ling, Clarence; Ermolenko, Dmitri N


    During protein synthesis, tRNA and mRNA are translocated from the A to P to E sites of the ribosome thus enabling the ribosome to translate one codon of mRNA after the other. Ribosome translocation along mRNA is induced by the universally conserved ribosome GTPase, elongation factor G (EF-G) in bacteria and elongation factor 2 (EF-2) in eukaryotes. Recent structural and single-molecule studies revealed that tRNA and mRNA translocation within the ribosome is accompanied by cyclic forward and reverse rotations between the large and small ribosomal subunits parallel to the plane of the intersubunit interface. In addition, during ribosome translocation, the 'head' domain of small ribosomal subunit undergoes forward- and back-swiveling motions relative to the rest of the small ribosomal subunit around the axis that is orthogonal to the axis of intersubunit rotation. tRNA/mRNA translocation is also coupled to the docking of domain IV of EF-G into the A site of the small ribosomal subunit that converts the thermally driven motions of the ribosome and tRNA into the forward translocation of tRNA/mRNA inside the ribosome. Despite recent and enormous progress made in the understanding of the molecular mechanism of ribosome translocation, the sequence of structural rearrangements of the ribosome, EF-G and tRNA during translocation is still not fully established and awaits further investigation. WIREs RNA 2016, 7:620-636. doi: 10.1002/wrna.1354 For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

  11. Orthogonality and Hecke operators

    Indian Academy of Sciences (India)


    Aug 26, 2016 ... Permanent link: Keywords. Hecke operator; eigenvalue; orthogonality; Atkin–Lehner theory. Abstract. In this article we analyze orthogonality relations between old forms and the connection to the theory of Hecke operators. Author Affiliations.

  12. Orthogonality and Hecke operators

    Indian Academy of Sciences (India)

    E-mail:; MS received 16 January 2006; revised 21 April 2009. Abstract. In this article we analyze orthogonality relations between old forms and the connection to the theory of Hecke operators. Keywords. Hecke operator; eigenvalue; orthogonality; Atkin–Lehner ...

  13. Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome (United States)

    Poirot, Olivier; Timsit, Youri


    From brain to the World Wide Web, information-processing networks share common scale invariant properties. Here, we reveal the existence of neural-like networks at a molecular scale within the ribosome. We show that with their extensions, ribosomal proteins form complex assortative interaction networks through which they communicate through tiny interfaces. The analysis of the crystal structures of 50S eubacterial particles reveals that most of these interfaces involve key phylogenetically conserved residues. The systematic observation of interactions between basic and aromatic amino acids at the interfaces and along the extension provides new structural insights that may contribute to decipher the molecular mechanisms of signal transmission within or between the ribosomal proteins. Similar to neurons interacting through “molecular synapses”, ribosomal proteins form a network that suggest an analogy with a simple molecular brain in which the “sensory-proteins” innervate the functional ribosomal sites, while the “inter-proteins” interconnect them into circuits suitable to process the information flow that circulates during protein synthesis. It is likely that these circuits have evolved to coordinate both the complex macromolecular motions and the binding of the multiple factors during translation. This opens new perspectives on nanoscale information transfer and processing.

  14. Orthogonal tensor decompositions

    Energy Technology Data Exchange (ETDEWEB)

    Tamara G. Kolda


    The authors explore the orthogonal decomposition of tensors (also known as multi-dimensional arrays or n-way arrays) using two different definitions of orthogonality. They present numerous examples to illustrate the difficulties in understanding such decompositions. They conclude with a counterexample to a tensor extension of the Eckart-Young SVD approximation theorem by Leibovici and Sabatier [Linear Algebra Appl. 269(1998):307--329].

  15. Coherent orthogonal polynomials

    Energy Technology Data Exchange (ETDEWEB)

    Celeghini, E., E-mail: [Dipartimento di Fisica, Università di Firenze and INFN–Sezione di Firenze, I50019 Sesto Fiorentino, Firenze (Italy); Olmo, M.A. del, E-mail: [Departamento de Física Teórica and IMUVA, Universidad de Valladolid, E-47005, Valladolid (Spain)


    We discuss a fundamental characteristic of orthogonal polynomials, like the existence of a Lie algebra behind them, which can be added to their other relevant aspects. At the basis of the complete framework for orthogonal polynomials we include thus–in addition to differential equations, recurrence relations, Hilbert spaces and square integrable functions–Lie algebra theory. We start here from the square integrable functions on the open connected subset of the real line whose bases are related to orthogonal polynomials. All these one-dimensional continuous spaces allow, besides the standard uncountable basis (|x〉), for an alternative countable basis (|n〉). The matrix elements that relate these two bases are essentially the orthogonal polynomials: Hermite polynomials for the line and Laguerre and Legendre polynomials for the half-line and the line interval, respectively. Differential recurrence relations of orthogonal polynomials allow us to realize that they determine an infinite-dimensional irreducible representation of a non-compact Lie algebra, whose second order Casimir C gives rise to the second order differential equation that defines the corresponding family of orthogonal polynomials. Thus, the Weyl–Heisenberg algebra h(1) with C=0 for Hermite polynomials and su(1,1) with C=−1/4 for Laguerre and Legendre polynomials are obtained. Starting from the orthogonal polynomials the Lie algebra is extended both to the whole space of the L{sup 2} functions and to the corresponding Universal Enveloping Algebra and transformation group. Generalized coherent states from each vector in the space L{sup 2} and, in particular, generalized coherent polynomials are thus obtained. -- Highlights: •Fundamental characteristic of orthogonal polynomials (OP): existence of a Lie algebra. •Differential recurrence relations of OP determine a unitary representation of a non-compact Lie group. •2nd order Casimir originates a 2nd order differential equation that defines

  16. Ribosomal history reveals origins of modern protein synthesis.

    Directory of Open Access Journals (Sweden)

    Ajith Harish

    Full Text Available The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17 and the oldest substructure (the ribosomal ratchet in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.

  17. Kosambi and Proper Orthogonal Decomposition

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 6. Kosambi and the Proper Orthogonal Decomposition. Roddam Narasimha. General ... Keywords. Proper orthogonal decomposition; Karhunen–Loéve expansion; statistics in function space; characteristic eddies; special calculating machines.

  18. Commandeering the Ribosome: Lessons Learned from Dicistroviruses about Translation. (United States)

    Kerr, Craig H; Jan, Eric


    To replicate, all viruses depend entirely on the enslavement of host cell ribosomes for their own advantage. To this end, viruses have evolved a multitude of translational strategies to usurp the ribosome. RNA-based structures known as internal ribosome entry sites (IRESs) are among the most notable mechanisms employed by viruses to seize host ribosomes. In this article, we spotlight the intergenic region IRES from the Dicistroviridae family of viruses and its importance as a model for IRES-dependent translation and in understanding fundamental properties of translation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. The Modular Adaptive Ribosome.

    Directory of Open Access Journals (Sweden)

    Anupama Yadav

    Full Text Available The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.

  20. Isolation of Plastid Ribosomes. (United States)

    Yamaguchi, Kenichi


    Plastid ribosomes are responsible for a large part of the protein synthesis in plant leaves, green algal cells, and the vast majority in the thalli of red algae. Plastid translation is necessary not only for photosynthesis but also for development/differentiation of plants and algae. While some isolated plastid ribosomes from a few green lineages have been characterized by biochemical and proteomic approaches, in-depth proteomics including analyses of posttranslational modifications and processing, comparative proteomics of plastid ribosomes isolated from the cells grown under different conditions, and those from different taxa are still to be carried out. Establishment of isolation methods for pure plastid ribosomes from a wider range of species would be beneficial to study the relationship between structure, function, and evolution of plastid ribosomes. Here I describe methodologies and provide example protocols for extraction and isolation of plastid ribosomes from a unicellular green alga (Chlamydomonas reinhardtii), a land plant (Arabidopsis thaliana), and a marine red macroalga (Pyropia yezoensis).

  1. Ribosome Profiling in Maize. (United States)

    Chotewutmontri, Prakitchai; Stiffler, Nicholas; Watkins, Kenneth P; Barkan, Alice


    Ribosome profiling (also known as Ribo-seq) provides a genome-wide, high-resolution, and quantitative accounting of mRNA segments that are occupied by ribosomes in vivo. The method has been used to address numerous questions in bacteria, yeast, and metazoa, but its application to questions in plant biology is just beginning. This chapter provides a detailed protocol for profiling ribosomes in plant leaf tissue. The method was developed and optimized with maize, but it has been used successfully with Arabidopsis and tobacco as well. The method captures ribosome footprints from the chloroplast and cytosol in the same preparation, but it is not optimal for detecting the footprints of mitochondrial ribosomes. The protocol is robust and simpler than many of the methods reported previously for ribosome profiling in plants.

  2. Ribosome biogenesis and cancer. (United States)

    Derenzini, Massimo; Montanaro, Lorenzo; Trerè, Davide


    There is growing evidence indicating that the human pathological conditions characterized by an up-regulated ribosome biogenesis are at an increased risk of cancer onset. At the basis of this relationship is the close interconnection between the ribosome biogenesis and cell proliferation. Cell proliferation-stimulating factors also stimulate ribosome production, while the ribosome biogenesis rate controls the cell cycle progression. The major tumour suppressor, the p53 protein, plays an important balancing role between the ribosome biogenesis rate and the cell progression through the cell cycle phases. The perturbation of ribosome biogenesis stabilizes and activates p53, with a consequent cell cycle arrest and/or apoptotic cell death, whereas an up-regulated ribosome production down-regulates p53 expression and activity, thus facilitating neoplastic transformation. In the present review we describe the interconnection between ribosome biogenesis and cell proliferation, while highlighting the mechanisms by which quantitative changes in ribosome biogenesis may induce cancer. Copyright © 2017 Elsevier GmbH. All rights reserved.

  3. Orthogonal serialisation for Haskell

    DEFF Research Database (Denmark)

    Berthold, Jost


    Data serialisation is a crucial feature of real-world programming languages, often provided by standard libraries or even built-in to the language. However, a number of questions arise when the language in question uses demand-driven evaluation and supports higher-order functions, as is the case...... support for parallel Haskell on distributed memory platforms. This serialisation has highly desirable and so-far unrivalled properties: it is truly orthogonal to evaluation and also does not require any type class mechanisms. Especially, (almost) any kind of value can be serialised, including functions...

  4. Galerkin orthogonal polynomials (United States)

    Livermore, Philip W.


    The Galerkin method offers a powerful tool in the solution of differential equations and function approximation on the real interval [-1, 1]. By expanding the unknown function in appropriately chosen global basis functions, each of which explicitly satisfies the given boundary conditions, in general this scheme converges exponentially fast and almost always supplies the most terse representation of a smooth solution. To date, typical schemes have been defined in terms of a linear combination of two Jacobi polynomials. However, the resulting functions do not inherit the expedient properties of the Jacobi polynomials themselves and the basis set will not only be non-orthogonal but may, in fact, be poorly conditioned. Using a Gram-Schmidt procedure, it is possible to construct, in an incremental fashion, polynomial basis sets that not only satisfy any linear homogeneous boundary conditions but are also orthogonal with respect to the general weighting function (1-x)α(1+x)β. However, as it stands, this method is not only cumbersome but does not provide the structure for general index n of the functions and obscures their dependence on the parameters (α,β). In this paper, it is shown that each of these Galerkin basis functions, as calculated by the Gram-Schmidt procedure, may be written as a linear combination of a small number of Jacobi polynomials with coefficients that can be determined. Moreover, this terse analytic representation reveals that, for large index, the basis functions behave asymptotically like the single Jacobi polynomial Pn(α,β)(x). This new result shows that such Galerkin bases not only retain exponential convergence but expedient function-fitting properties too, in much the same way as the Jacobi polynomials themselves. This powerful methodology of constructing Galerkin basis sets is illustrated by many examples, and it is shown how the results extend to polar geometries. In exploring more generalised definitions of orthogonality involving

  5. Fourier series in orthogonal polynomials

    CERN Document Server

    Osilenker, Boris


    This book presents a systematic course on general orthogonal polynomials and Fourier series in orthogonal polynomials. It consists of six chapters. Chapter 1 deals in essence with standard results from the university course on the function theory of a real variable and on functional analysis. Chapter 2 contains the classical results about the orthogonal polynomials (some properties, classical Jacobi polynomials and the criteria of boundedness).The main subject of the book is Fourier series in general orthogonal polynomials. Chapters 3 and 4 are devoted to some results in this topic (classical

  6. When ribosomes go bad: diseases of ribosome biogenesis. (United States)

    Freed, Emily F; Bleichert, Franziska; Dutca, Laura M; Baserga, Susan J


    Ribosomes are vital for cell growth and survival. Until recently, it was believed that mutations in ribosomes or ribosome biogenesis factors would be lethal, due to the essential nature of these complexes. However, in the last few decades, a number of diseases of ribosome biogenesis have been discovered. It remains a challenge in the field to elucidate the molecular mechanisms underlying them.

  7. Theoretical Models for Orthogonal Cutting

    DEFF Research Database (Denmark)

    De Chiffre, Leonardo

    This review of simple models for orthogonal cutting was extracted from: “L. De Chiffre: Metal Cutting Mechanics and Applications, D.Sc. Thesis, Technical University of Denmark, 1990.”......This review of simple models for orthogonal cutting was extracted from: “L. De Chiffre: Metal Cutting Mechanics and Applications, D.Sc. Thesis, Technical University of Denmark, 1990.”...

  8. A ribosome without RNA

    Directory of Open Access Journals (Sweden)

    Harold S Bernhardt


    Full Text Available It was Francis Crick who first asked why the ribosome contains so much RNA, and discussed the implications of this for the direct flow of genetic information from DNA to protein. Remarkable advances in our understanding of the ribosome and protein synthesis, including the recent publication of two mammalian mitochondrial ribosome structures, have shed new light on this intriguing aspect of evolution in molecular biology. We examine here whether RNA is indispensable for coded protein synthesis, or whether an all-protein ‘ribosome’ (or ‘synthosome’ might be possible, with a protein enzyme catalyzing peptide synthesis, and release factor-like protein adaptors able to read a message composed of deoxyribonucleotides. We also compare the RNA world hypothesis with the alternative ‘proteins first’ hypothesis in terms of their different understandings of the evolution of the ribosome, and whether this might have been preceded by an ancestral form of nonribosomal peptide synthesis catalyzed by protein enzymes.

  9. Some discrete multiple orthogonal polynomials


    Arvesú, J.; Coussement, J.; Van Assche, W.


    27 pages, no figures.-- MSC2000 codes: 33C45, 33C10, 42C05, 41A28.-- Issue title: "Proceedings of the 6th International Symposium on Orthogonal Polynomials, Special Functions and their Applications" (OPSFA-VI, Rome, Italy, 18-22 June 2001). MR#: MR1985676 (2004g:33015) Zbl#: Zbl 1021.33006 In this paper, we extend the theory of discrete orthogonal polynomials (on a linear lattice) to polynomials satisfying orthogonality conditions with respect to r positive discrete measures. First w...

  10. An introduction to orthogonal polynomials

    CERN Document Server

    Chihara, Theodore S


    Assuming no further prerequisites than a first undergraduate course in real analysis, this concise introduction covers general elementary theory related to orthogonal polynomials. It includes necessary background material of the type not usually found in the standard mathematics curriculum. Suitable for advanced undergraduate and graduate courses, it is also appropriate for independent study. Topics include the representation theorem and distribution functions, continued fractions and chain sequences, the recurrence formula and properties of orthogonal polynomials, special functions, and some

  11. Structures of eukaryotic ribosomal stalk proteins and its complex with trichosanthin, and their implications in recruiting ribosome-inactivating proteins to the ribosomes. (United States)

    Choi, Andrew K H; Wong, Eddie C K; Lee, Ka-Ming; Wong, Kam-Bo


    Ribosome-inactivating proteins (RIP) are RNA N-glycosidases that inactivate ribosomes by specifically depurinating a conserved adenine residue at the α-sarcin/ricin loop of 28S rRNA. Recent studies have pointed to the involvement of the C-terminal domain of the eukaryotic stalk proteins in facilitating the toxic action of RIPs. This review highlights how structural studies of eukaryotic stalk proteins provide insights into the recruitment of RIPs to the ribosomes. Since the C-terminal domain of eukaryotic stalk proteins is involved in specific recognition of elongation factors and some eukaryote-specific RIPs (e.g., trichosanthin and ricin), we postulate that these RIPs may have evolved to hijack the translation-factor-recruiting function of ribosomal stalk in reaching their target site of rRNA.

  12. The 100S ribosome: ribosomal hibernation induced by stress. (United States)

    Yoshida, Hideji; Wada, Akira


    One of the most important cellular events in all organisms is protein synthesis (translation), which is catalyzed by ribosomes. The regulation of translational activity is dependent on the environmental situation of the cell. A decrease in overall translation under stress conditions is mainly accompanied by the formation of functionally inactive 100S ribosomes in bacteria. The 100S ribosome is a dimer of two 70S ribosomes that is formed through interactions between their 30S subunits. Two mechanisms of 100S ribosome formation are known: one involving ribosome modulation factor (RMF) and short hibernation promoting factor (HPF) in a part of Gammaproteobacteria including Escherichia coli, and the other involving only long HPF in the majority of bacteria. The expression of RMF is regulated by ppGpp and cyclic AMP-cAMP receptor protein (cAMP-CRP) induced by amino acid starvation and glucose depletion, respectively. When stress conditions are removed, the 100S ribosome immediately dissociates into the active 70S ribosomes by releasing RMF. The stage in the ribosome cycle at which the ribosome loses translational activity is referred to as 'Hibernation'. The lifetime of cells that cannot form 100S ribosomes by deletion of the rmf gene is shorter than that of parental cells under stress conditions in E. coli. This fact indicates that the interconversion system between active 70S ribosomes and inactive 100S ribosomes is an important survival strategy for bacteria. © 2014 John Wiley & Sons, Ltd.

  13. Ribosomal genes in focus (United States)

    Koberna, Karel; Malínský, Jan; Pliss, Artem; Mašata, Martin; Večeřová, Jaromíra; Fialová, Markéta; Bednár, Jan; Raška, Ivan


    T he organization of transcriptionally active ribosomal genes in animal cell nucleoli is investigated in this study in order to address the long-standing controversy with regard to the intranucleolar localization of these genes. Detailed analyses of HeLa cell nucleoli include direct localization of ribosomal genes by in situ hybridization and their indirect localization via nascent ribosomal transcript mappings. On the light microscopy (LM) level, ribosomal genes map in 10–40 fluorescence foci per nucleus, and transcription activity is associated with most foci. We demonstrate that each nucleolar focus observed by LM corresponds, on the EM level, to an individual fibrillar center (FC) and surrounding dense fibrillar components (DFCs). The EM data identify the DFC as the nucleolar subcompartment in which rRNA synthesis takes place, consistent with detection of rDNA within the DFC. The highly sensitive method for mapping nascent transcripts in permeabilized cells on ultrastructural level provides intense and unambiguous clustered immunogold signal over the DFC, whereas very little to no label is detected over the FC. This signal is strongly indicative of nascent “Christmas trees” of rRNA associated with individual rDNA genes, sampled on the surface of thin sections. Stereological analysis of the clustered transcription signal further suggests that these Christmas trees may be contorted in space and exhibit a DNA compaction ratio on the order of 4–5.5. PMID:12034768

  14. Ribosomal Antibiotics: Contemporary Challenges

    Directory of Open Access Journals (Sweden)

    Tamar Auerbach-Nevo


    Full Text Available Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.

  15. Orthogonal Polynomials and Special Functions

    CERN Document Server

    Assche, Walter


    The set of lectures from the Summer School held in Leuven in 2002 provide an up-to-date account of recent developments in orthogonal polynomials and special functions, in particular for algorithms for computer algebra packages, 3nj-symbols in representation theory of Lie groups, enumeration, multivariable special functions and Dunkl operators, asymptotics via the Riemann-Hilbert method, exponential asymptotics and the Stokes phenomenon. The volume aims at graduate students and post-docs working in the field of orthogonal polynomials and special functions, and in related fields interacting with orthogonal polynomials, such as combinatorics, computer algebra, asymptotics, representation theory, harmonic analysis, differential equations, physics. The lectures are self-contained requiring only a basic knowledge of analysis and algebra, and each includes many exercises.

  16. Post-transcriptional regulation of ribosome biogenesis in yeast

    Directory of Open Access Journals (Sweden)

    Isabelle C. Kos-Braun


    Full Text Available Most microorganisms are exposed to the constantly and often rapidly changing environment. As such they evolved mechanisms to balance their metabolism and energy expenditure with the resources available to them. When resources become scarce or conditions turn out to be unfavourable for growth, cells reduce their metabolism and energy usage to survive. One of the major energy consuming processes in the cell is ribosome biogenesis. Unsurprisingly, cells encountering adverse conditions immediately shut down production of new ribosomes. It is well established that nutrient depletion leads to a rapid repression of transcription of the genes encoding ribosomal proteins, ribosome biogenesis factors as well as ribosomal RNA (rRNA. However, if pre-rRNA processing and ribosome assembly are regulated post-transcriptionally remains largely unclear. We have recently uncovered that the yeast Saccharomyces cerevisiae rapidly switches between two alternative pre-rRNA processing pathways depending on the environmental conditions. Our findings reveal a new level of complexity in the regulation of ribosome biogenesis.

  17. Ubiquitination of stalled ribosome triggers ribosome-associated quality control. (United States)

    Matsuo, Yoshitaka; Ikeuchi, Ken; Saeki, Yasushi; Iwasaki, Shintaro; Schmidt, Christian; Udagawa, Tsuyoshi; Sato, Fumiya; Tsuchiya, Hikaru; Becker, Thomas; Tanaka, Keiji; Ingolia, Nicholas T; Beckmann, Roland; Inada, Toshifumi


    Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.

  18. Maintaining evolvability. (United States)

    Crow, James F


    Although molecular methods, such as QTL mapping, have revealed a number of loci with large effects, it is still likely that the bulk of quantitative variability is due to multiple factors, each with small effect. Typically, these have a large additive component. Conventional wisdom argues that selection, natural or artificial, uses up additive variance and thus depletes its supply. Over time, the variance should be reduced, and at equilibrium be near zero. This is especially expected for fitness and traits highly correlated with it. Yet, populations typically have a great deal of additive variance, and do not seem to run out of genetic variability even after many generations of directional selection. Long-term selection experiments show that populations continue to retain seemingly undiminished additive variance despite large changes in the mean value. I propose that there are several reasons for this. (i) The environment is continually changing so that what was formerly most fit no longer is. (ii) There is an input of genetic variance from mutation, and sometimes from migration. (iii) As intermediate-frequency alleles increase in frequency towards one, producing less variance (as p --> 1, p(1 - p) --> 0), others that were originally near zero become more common and increase the variance. Thus, a roughly constant variance is maintained. (iv) There is always selection for fitness and for characters closely related to it. To the extent that the trait is heritable, later generations inherit a disproportionate number of genes acting additively on the trait, thus increasing genetic variance. For these reasons a selected population retains its ability to evolve. Of course, genes with large effect are also important. Conspicuous examples are the small number of loci that changed teosinte to maize, and major phylogenetic changes in the animal kingdom. The relative importance of these along with duplications, chromosome rearrangements, horizontal transmission and polyploidy

  19. GTPases and the origin of the ribosome

    Directory of Open Access Journals (Sweden)

    Smith Temple F


    Full Text Available Abstract Background This paper is an attempt to trace the evolution of the ribosome through the evolution of the universal P-loop GTPases that are involved with the ribosome in translation and with the attachment of the ribosome to the membrane. The GTPases involved in translation in Bacteria/Archaea are the elongation factors EFTu/EF1, the initiation factors IF2/aeIF5b + aeIF2, and the elongation factors EFG/EF2. All of these GTPases also contain the OB fold also found in the non GTPase IF1 involved in initiation. The GTPase involved in the signal recognition particle in most Bacteria and Archaea is SRP54. Results 1 The Elongation Factors of the Archaea based on structural considerations of the domains have the following evolutionary path: EF1→ aeIF2 → EF2. The evolution of the aeIF5b was a later event; 2 the Elongation Factors of the Bacteria based on the topological considerations of the GTPase domain have a similar evolutionary path: EFTu→ IF→2→EFG. These evolutionary sequences reflect the evolution of the LSU followed by the SSU to form the ribosome; 3 the OB-fold IF1 is a mimic of an ancient tRNA minihelix. Conclusion The evolution of translational GTPases of both the Archaea and Bacteria point to the evolution of the ribosome. The elongation factors, EFTu/EF1, began as a Ras-like GTPase bringing the activated minihelix tRNA to the Large Subunit Unit. The initiation factors and elongation factor would then have evolved from the EFTu/EF1 as the small subunit was added to the evolving ribosome. The SRP has an SRP54 GTPase and a specific RNA fold in its RNA component similar to the PTC. We consider the SRP to be a remnant of an ancient form of an LSU bound to a membrane. Reviewers This article was reviewed by George Fox, Leonid Mirny and Chris Sander.

  20. Orthogonal Polynomials and their Applications

    CERN Document Server

    Dehesa, Jesús; Marcellan, Francisco; Francia, José; Vinuesa, Jaime


    The Segovia meeting set out to stimulate an intensive exchange of ideas between experts in the area of orthogonal polynomials and its applications, to present recent research results and to reinforce the scientific and human relations among the increasingly international community working in orthogonal polynomials. This volume contains original research papers as well as survey papers about fundamental questions in the field (Nevai, Rakhmanov & López) and its relationship with other fields such as group theory (Koornwinder), Padé approximation (Brezinski), differential equations (Krall, Littlejohn) and numerical methods (Rivlin).

  1. Ribosome Assembly as Antimicrobial Target

    Directory of Open Access Journals (Sweden)

    Rainer Nikolay


    Full Text Available Many antibiotics target the ribosome and interfere with its translation cycle. Since translation is the source of all cellular proteins including ribosomal proteins, protein synthesis and ribosome assembly are interdependent. As a consequence, the activity of translation inhibitors might indirectly cause defective ribosome assembly. Due to the difficulty in distinguishing between direct and indirect effects, and because assembly is probably a target in its own right, concepts are needed to identify small molecules that directly inhibit ribosome assembly. Here, we summarize the basic facts of ribosome targeting antibiotics. Furthermore, we present an in vivo screening strategy that focuses on ribosome assembly by a direct fluorescence based read-out that aims to identify and characterize small molecules acting as primary assembly inhibitors.

  2. The Orthogonalization of Magnetic Systems

    DEFF Research Database (Denmark)

    Merayo, José M.G.; Primdahl, Fritz; Brauer, Peter


    The construction of an orthogonal reference frame based on a set of three skew axes for a magnetic coil system and a magnetic sensor is discussed and presented. For a skew system, it is possible to define the coil axes and the magnetic axes as a dual set of axes that are linked to the system...

  3. Towards orthogonal Haskell data serialisation

    DEFF Research Database (Denmark)

    Berthold, Jost


    This paper investigates a novel approach to serialisation of Haskell data structures with a high degree of flexibility, based on runtime support for parallel Haskell on distributed memory platforms. This serialisation has highly desirable and so-far unrivalled properties: it is truly orthogonal...... safety of the serialisation process, as well as application ideas....

  4. The ribosome challenge to the RNA world. (United States)

    Bowman, Jessica C; Hud, Nicholas V; Williams, Loren Dean


    An RNA World that predated the modern world of polypeptide and polynucleotide is one of the most widely accepted models in origin of life research. In this model, the translation system shepherded the RNA World into the extant biology of DNA, RNA, and protein. Here, we examine the RNA World Hypothesis in the context of increasingly detailed information available about the origins, evolution, functions, and mechanisms of the translation system. We conclude that the translation system presents critical challenges to RNA World Hypotheses. Firstly, a timeline of the RNA World is problematic when the ribosome is incorporated. The mechanism of peptidyl transfer of the ribosome appears distinct from evolved enzymes, signaling origins in a chemical rather than biological milieu. Secondly, we have no evidence that the basic biochemical toolset of life is subject to substantive change by Darwinian evolution, as required for the transition from the RNA world to extant biology. Thirdly, we do not see specific evidence for biological takeover of ribozyme function by protein enzymes. Finally, we can find no basis for preservation of the ribosome as ribozyme or the universality of translation, if it were the case that other information transducing ribozymes, such as ribozyme polymerases, were replaced by protein analogs and erased from the phylogenetic record. We suggest that an updated model of the RNA World should address the current state of knowledge of the translation system.

  5. Ribosome recycling induces optimal translation rate at low ribosomal availability. (United States)

    Marshall, E; Stansfield, I; Romano, M C


    During eukaryotic cellular protein synthesis, ribosomal translation is made more efficient through interaction between the two ends of the messenger RNA (mRNA). Ribosomes reaching the 3' end of the mRNA can thus recycle and begin translation again on the same mRNA, the so-called 'closed-loop' model. Using a driven diffusion lattice model of translation, we study the effects of ribosome recycling on the dynamics of ribosome flow and density on the mRNA. We show that ribosome recycling induces a substantial increase in ribosome current. Furthermore, for sufficiently large values of the recycling rate, the lattice does not transition directly from low to high ribosome density, as seen in lattice models without recycling. Instead, a maximal current phase becomes accessible for much lower values of the initiation rate, and multiple phase transitions occur over a wide region of the phase plane. Crucially, we show that in the presence of ribosome recycling, mRNAs can exhibit a peak in protein production at low values of the initiation rate, beyond which translation rate decreases. This has important implications for translation of certain mRNAs, suggesting that there is an optimal concentration of ribosomes at which protein synthesis is maximal, and beyond which translational efficiency is impaired. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  6. [Obtaining ribosome crystals in homogenates]. (United States)

    Bersani, F; Longo, I; Fanti, M; Pettazzoni, P


    Chick embryos are homogenized in order to analyse ribosome crystallization. Ribosome crystallization has been induced by hypothermic treatment in chick embryos homogenate. Tetramers and crystals were produced by gradually inducing the temperature over a span of 10 h to 4 degrees C. It has been observed that the concentration of KCl in the buffer is a critical point. It is suggested that the nuclear fraction is engaged in ribosome crystallization.

  7. Nucleolus: The ribosome factory

    Czech Academy of Sciences Publication Activity Database

    Cmarko, Dušan; Šmigová, J.; Minichová, L.; Popov, Alexey


    Roč. 23, č. 10 (2008), s. 1291-1298 ISSN 0213-3911 R&D Projects: GA ČR(CZ) GA304/06/1691 Grant - others:Wellcome Trust(XE) 075834/04/Z; GA MŠk(CZ) LC535; GA ČR(CZ) GA304/06/1662 Program:LC Institutional research plan: CEZ:AV0Z50110509 Keywords : nucleolus * nucleolar architecture * ribosome biogenesis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.194, year: 2008

  8. Orthogonality preserving infinite dimensional quadratic stochastic operators

    Energy Technology Data Exchange (ETDEWEB)

    Akın, Hasan [Department of Mathematics, Faculty of Education, Zirve University, Gaziantep, 27260 (Turkey); Mukhamedov, Farrukh [Department of Computational & Theoretical Sciences Faculty of Science, International Islamic University Malaysia P.O. Box, 141, 25710, Kuantan Pahang (Malaysia)


    In the present paper, we consider a notion of orthogonal preserving nonlinear operators. We introduce π-Volterra quadratic operators finite and infinite dimensional settings. It is proved that any orthogonal preserving quadratic operator on finite dimensional simplex is π-Volterra quadratic operator. In infinite dimensional setting, we describe all π-Volterra operators in terms orthogonal preserving operators.

  9. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling. (United States)

    Spealman, Pieter; Wang, Hao; May, Gemma; Kingsford, Carl; McManus, C Joel


    Recent technological advances (e.g., microarrays and massively parallel sequencing) have facilitated genome-wide measurement of many aspects of gene regulation. Ribosome profiling is a high-throughput sequencing method used to measure gene expression at the level of translation. This is accomplished by quantifying both the number of translating ribosomes and their locations on mRNA transcripts. The inventors of this approach have published several methods papers detailing its implementation and addressing the basics of ribosome profiling data analysis. Here we describe our lab's procedure, which differs in some respects from those published previously. In addition, we describe a data analysis pipeline, Ribomap, for ribosome profiling data. Ribomap allocates sequence reads to alternative mRNA isoforms, normalizes sequencing bias along transcripts using RNA-seq data, and outputs count vectors of per-codon ribosome occupancy for each transcript.

  10. Ribosomes as molecular energy machines. (United States)

    Kremen, A


    The idea that ribosomes operate as biological molecular energy machines offers an alternative description to that based on the assumption that the functionally important motions in ribosomes are only coupled to thermal degrees of freedom. The alternative model assumes that the energy gained in GTP cleavage generates in the ribosomal complex a localized metastable region temporarily not interacting with thermal motions. The metastable region may move along a definite pathway and in distinct sites promote irreversible logical operations involved in polypeptide biosynthesis. The new alternative represents a more complex and advanced algorithm offering advantages in speed, accuracy, more sophisticated control, and better resistance to various kinds of noise.

  11. Downlink Resource Allocation for Evolved UTRAN and WiMAX Cellular Systems

    NARCIS (Netherlands)

    Jorguseski, L.; Le, T.M.H.; Fledderus, E.R.; Prasad, R.


    The future broadband wireless cellular systems evolved UTRAN (E-UTRAN) and WiMAX are receiving a lot of interest in recent years. Both systems deploy orthogonal frequency division multiplex (OFDM) physical layer consisting of large number of mutually orthogonal sub-carriers. This physical layer

  12. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. (United States)

    Gagnon, Matthieu G; Seetharaman, Sai V; Bulkley, David; Steitz, Thomas A


    In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

  13. Structural Basis for the Rescue of Stalled Ribosomes: Structure of YaeJ Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gagnon, Matthieu G.; Seetharaman, Sai V.; Bulkley, David; Steitz, Thomas A. (Yale)


    In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA{sub i}{sup fMet} and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

  14. Orthogonal separations: Comparison of orthogonality metrics by statistical analysis. (United States)

    Schure, Mark R; Davis, Joe M


    Twenty orthogonality metrics (OMs) derived from convex hull, information theory, fractal dimension, correlation coefficients, nearest neighbor distances and bin-density techniques were calculated from a diverse group of 47 experimental two-dimensional (2D) chromatograms. These chromatograms comprise two datasets; one dataset is a collection of 2D chromatograms from Peter Carr's laboratory at the University of Minnesota, and the other dataset is based on pairs of one-dimensional chromatograms previously published by Martin Gilar and coworkers (Waters Corp.). The chromatograms were pooled to make a third or combined dataset. Cross-correlation results suggest that specific OMs are correlated within families of nearest neighbor methods, correlation coefficients and the information theory methods. Principal component analysis of the OMs show that none of the OMs stands out as clearly better at explaining the data variance than any another OM. Principal component analysis of individual chromatograms shows that different OMs favor certain chromatograms. The chromatograms exhibit a range of quality, as subjectively graded by nine experts experienced in 2D chromatography. The subjective (grading) evaluations were taken at two intervals per expert and demonstrated excellent consistency for each expert. Excellent agreement for both very good and very bad chromatograms was seen across the range of experts. However, evaluation uncertainty increased for chromatograms that were judged as average to mediocre. The grades were converted to numbers (percentages) for numerical computations. The percentages were correlated with OMs to establish good OMs for evaluating the quality of 2D chromatograms. Certain metrics correlate better than others. However, these results are not consistent across all chromatograms examined. Most of the nearest neighbor methods were observed to correlate poorly with the percentages. However, one method, devised by Clark and Evans, appeared to work

  15. Ribosome dynamics and the evolutionary history of ribosomes (United States)

    Fox, George E.; Paci, Maxim; Tran, Quyen; Petrov, Anton S.; Williams, Loren D.


    The ribosome is a dynamic nanomachine responsible for coded protein synthesis. Its major subsystems were essentially in place at the time of the last universal common ancestor (LUCA). Ribosome evolutionary history thus potentially provides a window into the pre- LUCA world. This history begins with the origins of the peptidyl transferase center where the actual peptide is synthesized and then continues over an extended timeframe as additional functional centers including the GTPase center are added. The large ribosomal RNAs (rRNAs) have grown over time by an accretion process and a model exists that proposes a relative age of each accreted element. We have compared atomic resolution ribosome structures before and after EF-G bound GTP hydrolysis and thereby identified the location of 23 pivot points in the large rRNAs that facilitate ribosome dynamics. Pivots in small subunit helices h28 and h44 appear to be especially central to the process and according to the accretion model significantly older than the other helices containing pivots. Overall, the results suggest that ribosomal dynamics occurred in two phases. In the first phase, an inherently mobile h28/h44 combination provided the flexibility needed to create a dynamic ribosome that was essentially a Brownian machine. This addition likely made coded peptide synthesis possible by facilitating movement of a primitive mRNA. During the second phase, addition of pivoting elements and the creation of a factor binding site allowed the regulation of the inherent motion created by h28/h44. All of these events likely occurred before LUCA.

  16. Orthogonality preserving property, Wigner equation, and stability

    Directory of Open Access Journals (Sweden)

    Chmieliński Jacek


    Full Text Available We deal with the stability of the orthogonality preserving property in the class of mappings phase-equivalent to linear or conjugate-linear ones. We give a characterization of approximately orthogonality preserving mappings in this class and we show some connections between the considered stability and the stability of the Wigner equation.

  17. Orthogonalization of regressors in FMRI models.

    Directory of Open Access Journals (Sweden)

    Jeanette A Mumford

    Full Text Available The occurrence of collinearity in fMRI-based GLMs (general linear models may reduce power or produce unreliable parameter estimates. It is commonly believed that orthogonalizing collinear regressors in the model will solve this problem, and some software packages apply automatic orthogonalization. However, the effects of orthogonalization on the interpretation of the resulting parameter estimates is widely unappreciated or misunderstood. Here we discuss the nature and causes of collinearity in fMRI models, with a focus on the appropriate uses of orthogonalization. Special attention is given to how the two popular fMRI data analysis software packages, SPM and FSL, handle orthogonalization, and pitfalls that may be encountered in their usage. Strategies are discussed for reducing collinearity in fMRI designs and addressing their effects when they occur.

  18. Structures and Ribosomal Interaction of Ribosome-Inactivating Proteins. (United States)

    Shi, Wei-Wei; Mak, Amanda Nga-Sze; Wong, Kam-Bo; Shaw, Pang-Chui


    Ribosome-inactivating proteins (RIPs) including ricin, Shiga toxin, and trichosanthin, are RNA N-glycosidases that depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. RIPs are grouped into three types according to the number of subunits and the organization of the precursor sequences. RIPs are two-domain proteins, with the active site located in the cleft between the N- and C-terminal domains. It has been found that the basic surface residues of the RIPs promote rapid and specific targeting to the ribosome and a number of RIPs have been shown to interact with the C-terminal regions of the P proteins of the ribosome. At present, the structural basis for the interaction of trichosanthin and ricin-A chain toward P2 peptide is known. This review surveys the structural features of the representative RIPs and discusses how they approach and interact with the ribosome.

  19. Evolvable synthetic neural system (United States)

    Curtis, Steven A. (Inventor)


    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  20. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation

    National Research Council Canada - National Science Library

    Jewett, Michael C; Fritz, Brian R; Timmerman, Laura E; Church, George M

    ...‐step co‐activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment...

  1. On orthogonality preserving quadratic stochastic operators

    Energy Technology Data Exchange (ETDEWEB)

    Mukhamedov, Farrukh; Taha, Muhammad Hafizuddin Mohd [Department of Computational and Theoretical Sciences, Faculty of Science International Islamic University Malaysia, P.O. Box 141, 25710 Kuantan, Pahang Malaysia (Malaysia)


    A quadratic stochastic operator (in short QSO) is usually used to present the time evolution of differing species in biology. Some quadratic stochastic operators have been studied by Lotka and Volterra. In the present paper, we first give a simple characterization of Volterra QSO in terms of absolutely continuity of discrete measures. Further, we introduce a notion of orthogonal preserving QSO, and describe such kind of operators defined on two dimensional simplex. It turns out that orthogonal preserving QSOs are permutations of Volterra QSO. The associativity of genetic algebras generated by orthogonal preserving QSO is studied too.

  2. Challenges in describing ribosome dynamics (United States)

    Nguyen, Kien; Whitford, Paul Charles


    For decades, protein folding and functional dynamics have been described in terms of diffusive motion across an underlying energy landscape. With continued advances in structural biology and high-performance computing, the field is positioned to extend these approaches to large biomolecular assemblies. Through the application of energy landscape techniques to the ribosome, one may work towards establishing a comprehensive description of the dynamics, which will bridge theoretical concepts and experimental observations. In this perspective, we discuss a few of the challenges that will need to be addressed as we extend the application of landscape principles to the ribosome.

  3. Steinitz theorems for simple orthogonal polyhedra

    Directory of Open Access Journals (Sweden)

    David Eppstein


    Full Text Available We define a simple orthogonal polyhedron to be a three-dimensional polyhedron with the topology of a sphere in which three mutually-perpendicular edges meet at each vertex.By analogy to Steinitz's theorem characterizing the graphs of convex polyhedra, we find graph-theoretic characterizations of three classes of simple orthogonal polyhedra: corner polyhedra, which can be drawn by isometric projection in the plane with only one hidden vertex, xyz polyhedra, in which each axis-parallel line through a vertex contains exactly one other vertex, and arbitrary simple orthogonal polyhedra. In particular, the graphs of xyz polyhedra are exactly the bipartite cubic polyhedral graphs, and every bipartite cubic polyhedral graph with a 4-connected dual graph is the graph of a corner polyhedron. Based on our characterizations we find efficient algorithms for constructing orthogonal polyhedra from their graphs.

  4. Orthogonal photoswitching in a multifunctional molecular system

    National Research Council Canada - National Science Library

    Lerch, Michael M; Hansen, Mickel J; Velema, Willem A; Szymanski, Wiktor; Feringa, Ben L


    ... cleavage of photo-removable protecting groups. Here we report the orthogonal and reversible control of two distinct types of photoswitches in one solution, that is, a donor-acceptor Stenhouse adduct (DASA) and an azobenzene...

  5. Orthogonal Chirp-Based Ultrasonic Positioning. (United States)

    Khyam, Mohammad Omar; Ge, Shuzhi Sam; Li, Xinde; Pickering, Mark


    This paper presents a chirp based ultrasonic positioning system (UPS) using orthogonal chirp waveforms. In the proposed method, multiple transmitters can simultaneously transmit chirp signals, as a result, it can efficiently utilize the entire available frequency spectrum. The fundamental idea behind the proposed multiple access scheme is to utilize the oversampling methodology of orthogonal frequency-division multiplexing (OFDM) modulation and orthogonality of the discrete frequency components of a chirp waveform. In addition, the proposed orthogonal chirp waveforms also have all the advantages of a classical chirp waveform. Firstly, the performance of the waveforms is investigated through correlation analysis and then, in an indoor environment, evaluated through simulations and experiments for ultrasonic (US) positioning. For an operational range of approximately 1000 mm, the positioning root-mean-square-errors (RMSEs) &90% error were 4.54 mm and 6.68 mm respectively.

  6. Adaptive and Approximate Orthogonal Range Counting

    DEFF Research Database (Denmark)

    Chan, Timothy M.; Wilkinson, Bryan Thomas


    ]. •We give an O(n loglog n)-space data structure for approximate 2-D orthogonal range counting that can compute a (1+δ)-factor approximation to the count in O(loglog n) time for any fixed constant δ>0. Again, our bounds match the state of the art for the 2-D orthogonal range emptiness problem. •Lastly...

  7. Sign patterns of J-orthogonal matrices

    Czech Academy of Sciences Publication Activity Database

    Hall, F.J.; Li, Z.; Parnass, C.; Rozložník, Miroslav


    Roč. 5, č. 1 (2017), s. 225-241 ISSN 2300-7451 Institutional support: RVO:67985840 Keywords : G-matrix * J-orthogonal matrix * sign pattern matrix * sign patterns that allow J-orthogonality Subject RIV: BA - General Mathematics xml ?format=INT

  8. An orthogonal DNA replication system in yeast. (United States)

    Ravikumar, Arjun; Arrieta, Adrian; Liu, Chang C


    An extranuclear replication system, consisting of an orthogonal DNA plasmid-DNA polymerase pair, was developed in Saccharomyces cerevisiae. Engineered error-prone DNA polymerases showed complete mutational targeting in vivo: per-base mutation rates on the plasmid were increased substantially and remained stable with no increase in genomic rates. Orthogonal replication serves as a platform for in vivo continuous evolution and as a system whose replicative properties can be manipulated independently of the host's.

  9. Studies on Pea Ribosomal Proteins (United States)

    Lin, Chu-Yung; Chia, Subrina Li-Li; Travis, Robert L.; Key, Joe L.


    Ribosomal subunits prepared by NH4Cl dissociation (0.5 m) of the monomeric ribosomes were much less active in in vitro protein synthesis than those prepared by KCl dissociation. The decrease in activity correlated with a detachment of some proteins (L2 and L9 as shown by gel electrophoresis) within the 60S ribosomal subunits. Subunits prepared with 0.3 m NH4Cl retained L2 and L9, but the activity remained low. Incubation of these 60S subunits in TKM buffer (50 mm tris [pH 7.5], 20 mm KCl, and 5 mm MgCl2) for 20 min at 37 C restored the activity almost to the level of those obtained by KCl dissociation. Treatment of the 0.3 m NH4Cl-derived 60S subunits with a protein reagent, Procion brilliant blue, prior to extraction of the ribosomal proteins resulted in the loss of L2 and L9, showing that these proteins were made accessible for dye binding. These observations suggest that a considerable degree of unfolding of the 60S subunit occurs at 0.3 m NH4Cl (this apparently leads to a preferential detachment of L2 and L9 at 0.5 m NH4Cl) and that the activity of the purified subunits depends not only on the presence of L2 and L9 but also on the organization of these proteins within the 60S subunits. Images PMID:16659254


    This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

  11. The ribosome modulation factor (RMF) binding site on the 100S ribosome of Escherichia coli. (United States)

    Yoshida, Hideji; Maki, Yasushi; Kato, Hisako; Fujisawa, Hisao; Izutsu, Kaori; Wada, Chieko; Wada, Akira


    During the stationary growth phase, Escherichia coli 70S ribosomes are converted to 100S ribosomes, and translational activity is lost. This conversion is caused by the binding of the ribosome modulation factor (RMF) to 70S ribosomes. In order to elucidate the mechanisms by which 100S ribosomes form and translational inactivation occurs, the shape of the 100S ribosome and the RMF ribosomal binding site were investigated by electron microscopy and protein-protein cross-linking, respectively. We show that (i) the 100S ribosome is formed by the dimerization of two 70S ribosomes mediated by face-to-face contacts between their constituent 30S subunits, and (ii) RMF binds near the ribosomal proteins S13, L13, and L2. The positions of these proteins indicate that the RMF binding site is near the peptidyl transferase center or the P site (peptidyl-tRNA binding site). These observations are consistent with the translational inactivation of the ribosome by RMF binding. After the "Recycling" stage, ribosomes can readily proceed to the "Initiation" stage during exponential growth, but during stationary phase, the majority of 70S ribosomes are stored as 100S ribosomes and are translationally inactive. We suggest that this conversion of 70S to 100S ribosomes represents a newly identified stage of the ribosomal cycle in stationary phase cells, and we have termed it the "Hibernation" stage.

  12. A liaison between mTOR signaling, ribosome biogenesis and cancer. (United States)

    Gentilella, Antonio; Kozma, Sara C; Thomas, George


    The ability to translate genetic information into functional proteins is considered a landmark in evolution. Ribosomes have evolved to take on this responsibility and, although there are some differences in their molecular make-up, both prokaryotes and eukaryotes share a common structural architecture and similar underlying mechanisms of protein synthesis. Understanding ribosome function and biogenesis has been the focus of extensive research since the early days of their discovery. In the last decade however, new and unexpected roles have emerged that place deregulated ribosome biogenesis and protein synthesis at the crossroads of pathological settings, particularly cancer, revealing a set of novel cellular checkpoints. Moreover, it is also becoming evident that mTOR signaling, which regulates an array of anabolic processes, including ribosome biogenesis, is often exploited by cancer cells to sustain proliferation through the upregulation of global protein synthesis. The use of pharmacological agents that interfere with ribosome biogenesis and mTOR signaling has proven to be an effective strategy to control cancer development clinically. Here we discuss the most recent findings concerning the underlying mechanisms by which mTOR signaling controls ribosome production and the potential impact of ribosome biogenesis in tumor development. This article is part of a Special Issue entitled: Translation and Cancer. Copyright © 2015. Published by Elsevier B.V.

  13. Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome. (United States)

    Li, Xiaojun; Sun, Qingan; Jiang, Cai; Yang, Kailu; Hung, Li-Wei; Zhang, Junjie; Sacchettini, James C


    The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. 5S rRNA and ribosome. (United States)

    Gongadze, G M


    5S rRNA is an integral component of the ribosome of all living organisms. It is known that the ribosome without 5S rRNA is functionally inactive. However, the question about the specific role of this RNA in functioning of the translation apparatus is still open. This review presents a brief history of the discovery of 5S rRNA and studies of its origin and localization in the ribosome. The previously expressed hypotheses about the role of this RNA in the functioning of the ribosome are discussed considering the unique location of 5S rRNA in the ribosome and its intermolecular contacts. Based on analysis of the current data on ribosome structure and its functional complexes, the role of 5S rRNA as an intermediary between ribosome functional domains is discussed.

  15. Ribosomal targets for antibiotic drug discovery

    Energy Technology Data Exchange (ETDEWEB)

    Blanchard, Scott C.; Feldman, Michael Brian; Wang, Leyi; Doudna Cate, James H.; Pulk, Arto; Altman, Roger B.; Wasserman, Michael R


    The present invention relates to methods to identify molecules that binds in the neomycin binding pocket of a bacterial ribosome using structures of an intact bacterial ribosome that reveal how the ribosome binds tRNA in two functionally distinct states, determined by x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor (RRF) and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit (P/E) site. Additionally, the invention relates to various assays, including single-molecule assay for ribosome recycling, and methods to identify compounds that interfere with ribosomal function by detecting newly identified intermediate FRET states using known and novel FRET pairs on the ribosome. The invention also provides vectors and compositions with an N-terminally tagged S13 protein.

  16. The ribosome regulates flavodoxin folding


    Houwman, Joseline A.


    During and after their translation by the ribosome, folding of polypeptides to biologically active proteins is of vital importance for all living organisms. Gaining knowledge about nascent chain folding is required to enhance our understanding of protein folding in the cell. This in turn allows us to obtain insights into factors responsible for protein misfolding, aggregation, and, potentially, for numerous devastating pathologies. In Chapter 1 the model protein flavodoxin is introduced. Also...

  17. Local indistinguishability of multipartite orthogonal product bases (United States)

    Xu, Guang-Bao; Wen, Qiao-Yan; Gao, Fei; Qin, Su-Juan; Zuo, Hui-Juan


    So far, very little is known about local indistinguishability of multipartite orthogonal product bases except some special cases. We first give a method to construct an orthogonal product basis with n parties each holding a 1/2(n+1)-dimensional system, where n≥5 and n is odd. The proof of the local indistinguishability of the basis exhibits that it is a sufficient condition for the local indistinguishability of an orthogonal multipartite product basis that all the positive operator-valued measure elements of each party can only be proportional to the identity operator to make further discrimination feasible. Then, we construct a set of n-partite product states, which contains only 2 n members and cannot be perfectly distinguished by local operations and classic communication. All the results lead to a better understanding of the phenomenon of quantum nonlocality without entanglement in multipartite and high-dimensional quantum systems.

  18. Repurposing ribosomes for synthetic biology. (United States)

    Liu, Yi; Kim, Do Soon; Jewett, Michael C


    The translation system is the cell's factory for protein biosynthesis, stitching together hundreds to thousands of amino acids into proteins, which are required for the structure, function, and regulation of living systems. The extraordinary synthetic capability of this system, which includes the ribosome and its associated factors required for polymerization, has driven extensive efforts to harness it for societal use in areas as diverse as energy, materials, and medicine. A powerful example is recombinant protein production, which has impacted the lives of patients through the synthesis of biopharmaceuticals such as insulin. In nature, however, only limited sets of monomers are utilized, thereby resulting in limited sets of biopolymers (i.e., proteins). Expanding nature's repertoire of ribosomal monomers could yield new classes of enzymes, therapeutics, materials, and chemicals with diverse, genetically encoded chemistry. Here, we discuss recent progress towards engineering ribosomes both in vivo and in vitro. These fundamental and technical breakthroughs open doors for advanced applications in biotechnology and synthetic biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. (United States)

    Jakob, Steffen; Ohmayer, Uli; Neueder, Andreas; Hierlmeier, Thomas; Perez-Fernandez, Jorge; Hochmuth, Eduard; Deutzmann, Rainer; Griesenbeck, Joachim; Tschochner, Herbert; Milkereit, Philipp


    Early steps of eukaryotic ribosome biogenesis require a large set of ribosome biogenesis factors which transiently interact with nascent rRNA precursors (pre-rRNA). Most likely, concomitant with that initial contacts between ribosomal proteins (r-proteins) and ribosome precursors (pre-ribosomes) are established which are converted into robust interactions between pre-rRNA and r-proteins during the course of ribosome maturation. Here we analysed the interrelationship between r-protein assembly events and the transient interactions of ribosome biogenesis factors with early pre-ribosomal intermediates termed 90S pre-ribosomes or small ribosomal subunit (SSU) processome in yeast cells. We observed that components of the SSU processome UTP-A and UTP-B sub-modules were recruited to early pre-ribosomes independently of all tested r-proteins. On the other hand, groups of SSU processome components were identified whose association with early pre-ribosomes was affected by specific r-protein assembly events in the head-platform interface of the SSU. One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain. Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes. They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.

  20. High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome. (United States)

    Giavalisco, Patrick; Wilson, Daniel; Kreitler, Thomas; Lehrach, Hans; Klose, Joachim; Gobom, Johan; Fucini, Paola


    Proteomic studies have addressed the composition of plant chloroplast ribosomes and 70S ribosomes from the unicellular organism Chlamydomonas reinhardtii But comprehensive characterization of cytoplasmic 80S ribosomes from higher plants has been lacking. We have used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to analyse the cytoplasmic 80S ribosomes from the model flowering plant Arabidopsis thaliana. Of the 80 ribosomal protein families predicted to comprise the cytoplasmic 80S ribosome, we have confirmed the presence of 61; specifically, 27 (84%) of the small 40S subunit and 34 (71%) of the large 60S subunit. Nearly half (45%) of the ribosomal proteins identified are represented by two or more distinct spots in the 2-DE gel indicating that these proteins are either post-translationally modified or present as different isoforms. Consistently, MS-based protein identification revealed that at least one-third (34%) of the identified ribosomal protein families showed expression of two or more family members. In addition, we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation suggesting their possible association with the 80S ribosomes. Among them, RACK1 has recently been proposed to be a ribosome-associated protein that promotes efficient translation in yeast. The study, thus provides the basis for further investigation into the function of the other identified non-ribosomal proteins as well as the biological meaning of the various ribosomal protein isoforms.

  1. Orthogonal control of antibacterial activity with light. (United States)

    Velema, Willem A; van der Berg, Jan Pieter; Szymanski, Wiktor; Driessen, Arnold J M; Feringa, Ben L


    Selection of a single bacterial strain out of a mixture of microorganisms is of crucial importance in healthcare and microbiology research. Novel approaches that can externally control bacterial selection are a valuable addition to the microbiology toolbox. In this proof-of-concept, two complementary antibiotics are protected with photocleavable groups that can be orthogonally addressed with different wavelengths of light. This allows for the light-triggered selection of a single bacterial strain out of a mixture of multiple strains, by choosing the right wavelength. Further improvement toward additional orthogonally addressable antibiotics might ultimately lead to a novel methodology for bacterial selection in complex populations.

  2. Riemannian geometry in an orthogonal frame

    CERN Document Server

    Cartan, Elie Joseph


    Foreword by S S Chern. In 1926-27, Cartan gave a series of lectures in which he introduced exterior forms at the very beginning and used extensively orthogonal frames throughout to investigate the geometry of Riemannian manifolds. In this course he solved a series of problems in Euclidean and non-Euclidean spaces, as well as a series of variational problems on geodesics. In 1960, Sergei P Finikov translated from French into Russian his notes of these Cartan's lectures and published them as a book entitled Riemannian Geometry in an Orthogonal Frame. This book has many innovations, such as the n

  3. Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell

    Directory of Open Access Journals (Sweden)

    Jékely Gáspár


    Full Text Available Abstract Background The origin of the nucleus is a central problem about the origin of eukaryotes. The common ancestry of nuclear pore complexes (NPC and vesicle coating complexes indicates that the nucleus evolved via the modification of a pre-existing endomembrane system. Such an autogenous scenario is cell biologically feasible, but it is not clear what were the selective or neutral mechanisms that had led to the origin of the nuclear compartment. Results A key selective force during the autogenous origin of the nucleus could have been the need to segregate ribosome factories from the cytoplasm where ribosomal proteins (RPs of the protomitochondrium were synthesized. After its uptake by an anuclear cell the protomitochondrium transferred several of its RP genes to the host genome. Alphaproteobacterial RPs and archaebacterial-type host ribosomes were consequently synthesized in the same cytoplasm. This could have led to the formation of chimeric ribosomes. I propose that the nucleus evolved when the host cell compartmentalised its ribosome factories and the tightly linked genome to reduce ribosome chimerism. This was achieved in successive stages by first evolving karyopherin and RanGTP dependent chaperoning of RPs, followed by the evolution of a membrane network to serve as a diffusion barrier, and finally a hydrogel sieve to ensure selective permeability at nuclear pores. Computer simulations show that a gradual segregation of cytoplasm and nucleoplasm via these steps can progressively reduce ribosome chimerism. Conclusion Ribosome chimerism can provide a direct link between the selective forces for and the mechanisms of evolving nuclear transport and compartmentalisation. The detailed molecular scenario presented here provides a solution to the gradual evolution of nuclear compartmentalization from an anuclear stage. Reviewers This article was reviewed by Eugene V Koonin, Martijn Huynen, Anthony M. Poole and Patrick Forterre.

  4. Ribosome engineering to promote new crystal forms

    Energy Technology Data Exchange (ETDEWEB)

    Selmer, Maria, E-mail: [Uppsala University, Box 596, SE-751 24 Uppsala (Sweden); MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Gao, Yong-Gui; Weixlbaumer, Albert; Ramakrishnan, V., E-mail: [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Uppsala University, Box 596, SE-751 24 Uppsala (Sweden)


    Truncation of ribosomal protein L9 in T. thermophilus allows the generation of new crystal forms and the crystallization of ribosome–GTPase complexes. Crystallographic studies of the ribosome have provided molecular details of protein synthesis. However, the crystallization of functional complexes of ribosomes with GTPase translation factors proved to be elusive for a decade after the first ribosome structures were determined. Analysis of the packing in different 70S ribosome crystal forms revealed that regardless of the species or space group, a contact between ribosomal protein L9 from the large subunit and 16S rRNA in the shoulder of a neighbouring small subunit in the crystal lattice competes with the binding of GTPase elongation factors to this region of 16S rRNA. To prevent the formation of this preferred crystal contact, a mutant strain of Thermus thermophilus, HB8-MRCMSAW1, in which the ribosomal protein L9 gene has been truncated was constructed by homologous recombination. Mutant 70S ribosomes were used to crystallize and solve the structure of the ribosome with EF-G, GDP and fusidic acid in a previously unobserved crystal form. Subsequent work has shown the usefulness of this strain for crystallization of the ribosome with other GTPase factors.

  5. On ribosome load, codon bias and protein abundance.

    Directory of Open Access Journals (Sweden)

    Stefan Klumpp

    Full Text Available Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

  6. Dynamic evolution of mitochondrial ribosomal proteins in Holozoa. (United States)

    Scheel, Bettina M; Hausdorf, Bernhard


    We studied the highly dynamic evolution of mitochondrial ribosomal proteins (MRPs) in Holozoa. Most major clades within Holozoa are characterized by gains and/or losses of MRPs. The usefulness of gains of MRPs as rare genomic changes in phylogenetics is undermined by the high frequency of secondary losses. However, phylogenetic analyses of the MRP sequences provide evidence for the Acrosomata hypothesis, a sister group relationship between Ctenophora and Bilateria. An extensive restructuring of the mitochondrial genome and, as a consequence, of the mitochondrial ribosomes occurred in the ancestor of metazoans. The last MRP genes encoded in the mitochondrial genome were either moved to the nuclear genome or were lost. The strong decrease in size of the mitochondrial genome was probably caused by selection for rapid replication of mitochondrial DNA during oogenesis in the metazoan ancestor. A phylogenetic analysis of MRPL56 sequences provided evidence for a horizontal gene transfer of the corresponding MRP gene between metazoans and Dictyostelidae (Amoebozoa). The hypothesis that the requisition of additional MRPs compensated for a loss of rRNA segments in the mitochondrial ribosomes is corroborated by a significant negative correlation between the number of MRPs and length of the rRNA. Newly acquired MRPs evolved faster than bacterial MRPs and positions in eukaryote-specific MRPs were more strongly affected by coevolution than positions in prokaryotic MRPs in accordance with the necessity to fit these proteins into the pre-existing structure of the mitoribosome. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Hyperkahler cones and orthogonal Wolf spaces

    NARCIS (Netherlands)

    Anguelova, L.K.; Rocek, M.; Vandoren, S.


    We construct the hyperk¨ahler cones corresponding to the quaternion-K¨ahler orthogonal Wolf spaces SO(n+4)/ SO(n)×SO(4) and their non-compact versions, which appear in hypermultiplet couplings to N = 2 supergravity. The geometry is completely encoded by a single function, the hyperk¨ahler

  8. Hodograph method in MHD orthogonal fluid flows

    Directory of Open Access Journals (Sweden)

    P. V. Nguyen


    Full Text Available Equations for steady plane MHD orthogonal flows of a viscous incompressible fluid of finite electrical conductivity are recast in the hodograph plane by using the Legendre transform function of the streamfunction. Three examples are studied to illustrate the developed theory. Solutions and geometries for these examples are determined.

  9. Comparison of Orthogonal Matching Pursuit Implementations

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Christensen, Mads Græsbøll


    We study the numerical and computational performance of three implementations of orthogonal matching pursuit: one using the QR matrix decomposition, one using the Cholesky matrix decomposition, and one using the matrix inversion lemma. We find that none of these implementations suffer from...

  10. Orthogonal antenna architecture for MIMO handsets

    DEFF Research Database (Denmark)

    Tatomirescu, Alexandru; Alrabadi, Osama; Pedersen, Gert Frølund


    The paper presents a method for decorrelating the antenna elements of a MIMO system in a compact handheld terminal at low bands. The architecture of the antenna system induces orthogonal currents over the closely spaced antennas resulting in a correlation free system. Nevertheless, due to the small...

  11. A new description of orthogonal bases

    NARCIS (Netherlands)

    Coecke, Bob; Pavlovic, Dusko; Vicary, Jamie


    We show that an orthogonal basis for a finite-dimensional Hilbert space can be equivalently characterised as a commutative †-Frobenius monoid in the category FdHilb, which has finite-dimensional Hilbert spaces as objects and continuous linear maps as morphisms, and tensor product for the monoidal

  12. Optimal Planar Orthogonal Skyline Counting Queries

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Larsen, Kasper Green


    The skyline of a set of points in the plane is the subset of maximal points, where a point (x,y) is maximal if no other point (x',y') satisfies x'≥ x and y'≥ x. We consider the problem of preprocessing a set P of n points into a space efficient static data structure supporting orthogonal skyline...

  13. New data structures for orthogonal range searching

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Brodal, Gerth Stølting; Rauhe, Theis


    We present new general techniques for static orthogonal range searching problems in two and higher dimensions. For the general range reporting problem in R3, we achieve query time O(log n+k) using space O(n log1+ε n), where n denotes the number of stored points and k the number of points to be re...

  14. Structural Basis for Ribosome Rescue in Bacteria. (United States)

    Huter, Paul; Müller, Claudia; Arenz, Stefan; Beckert, Bertrand; Wilson, Daniel N


    Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Ribosome Collision Is Critical for Quality Control during No-Go Decay. (United States)

    Simms, Carrie L; Yan, Liewei L; Zaher, Hani S


    No-go decay (NGD) is a eukaryotic quality control mechanism that evolved to cope with translational arrests. The process is characterized by an endonucleolytic cleavage near the stall sequence, but the mechanistic details are unclear. Our analysis of cleavage sites indicates that cleavage requires multiple ribosomes on the mRNA. We also show that reporters harboring stall sequences near the initiation codon, which cannot accommodate multiple ribosomes, are not subject to NGD. Consistent with our model, we uncover an inverse correlation between ribosome density per mRNA and cleavage efficiency. Furthermore, promoting global ribosome collision in vivo resulted in ubiquitination of ribosomal proteins, suggesting that collision is sensed by the cell to initiate downstream quality control processes. Collectively, our data suggest that NGD and subsequent quality control are triggered by ribosome collision. This model provides insight into the regulation of quality control processes and the manner by which they reduce off-target effects. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Ribosomes are optimized for autocatalytic production (United States)

    Reuveni, Shlomi; Ehrenberg, Måns; Paulsson, Johan


    Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control. Here we demonstrate mathematically that many less well understood, larger-scale features of ribosomes—such as why a few ribosomal RNA molecules dominate the mass and why the ribosomal protein content is divided into 55-80 small, similarly sized segments—speed up their autocatalytic production.

  17. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. (United States)

    Woolford, John L; Baserga, Susan J


    Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (>5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes.

  18. Evolving digital ecological networks.

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna

    Full Text Available "It is hard to realize that the living world as we know it is just one among many possibilities" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism. Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved.

  19. On the mod p reduction of orthogonal representations


    Serre, Jean-Pierre


    We show that the reduction mod p of an orthogonal linear representation is orthogonal, and we generalize this fact to representations of algebras with involution.The proofs make an essential use of the notion of " middle lattices ".

  20. Duality of orthogonal polynomials on a finite set


    Borodin, Alexei


    We prove a certain duality relation for orthogonal polynomials defined on a finite set. The result is used in a direct proof of the equivalence of two different ways of computing the correlation functions of a discrete orthogonal polynomial ensemble.

  1. Orthogonal Range Searching on the RAM, Revisited

    DEFF Research Database (Denmark)

    Chan, Timothy M.; Larsen, Kasper Green; Patrascu, Mihai


    We present a number of new results on one of the most extensively studied topics in computational geometry, orthogonal range searching. All our results are in the standard word RAM model: We present two data structures for 2-d orthogonal range emptiness. The first achieves O(n lg lg n) space and O...... the output size. This resolves two open problems (both appeared in Preparata and Shamos' seminal book): given a set of n axis-aligned rectangles in the plane, we can report all k enclosure pairs (i.e., pairs (r1,r2) where rectangle r1 completely encloses rectangle r2) in O(n lg n + k) expected time; given...

  2. Orthogonal photoswitching in a multifunctional molecular system. (United States)

    Lerch, Michael M; Hansen, Mickel J; Velema, Willem A; Szymanski, Wiktor; Feringa, Ben L


    The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely on wavelength-selective cleavage of photo-removable protecting groups. Here we report the orthogonal and reversible control of two distinct types of photoswitches in one solution, that is, a donor-acceptor Stenhouse adduct (DASA) and an azobenzene. The control is achieved by using three different wavelengths of irradiation and a thermal relaxation process. The reported combination tolerates a broad variety of differently substituted photoswitches. The presented system is also extended to an intramolecular combination of photoresponsive units. A model application for an intramolecular combination of switches is presented, in which the DASA component acts as a phase-transfer tag, while the azobenzene moiety independently controls the binding to α-cyclodextrin.

  3. HOLA: Human-like Orthogonal Network Layout. (United States)

    Kieffer, Steve; Dwyer, Tim; Marriott, Kim; Wybrow, Michael


    Over the last 50 years a wide variety of automatic network layout algorithms have been developed. Some are fast heuristic techniques suitable for networks with hundreds of thousands of nodes while others are multi-stage frameworks for higher-quality layout of smaller networks. However, despite decades of research currently no algorithm produces layout of comparable quality to that of a human. We give a new "human-centred" methodology for automatic network layout algorithm design that is intended to overcome this deficiency. User studies are first used to identify the aesthetic criteria algorithms should encode, then an algorithm is developed that is informed by these criteria and finally, a follow-up study evaluates the algorithm output. We have used this new methodology to develop an automatic orthogonal network layout method, HOLA, that achieves measurably better (by user study) layout than the best available orthogonal layout algorithm and which produces layouts of comparable quality to those produced by hand.

  4. The Fractional Orthogonal Difference with Applications

    Directory of Open Access Journals (Sweden)

    Enno Diekema


    Full Text Available This paper is a follow-up of a previous paper of the author published in Mathematics journal in 2015, which treats the so-called continuous fractional orthogonal derivative. In this paper, we treat the discrete case using the fractional orthogonal difference. The theory is illustrated with an application of a fractional differentiating filter. In particular, graphs are presented of the absolutel value of the modulus of the frequency response. These make clear that for a good insight into the behavior of a fractional differentiating filter, one has to look for the modulus of its frequency response in a log-log plot, rather than for plots in the time domain.

  5. Expression of strain tensor in orthogonal curvilinear coordinates

    Directory of Open Access Journals (Sweden)

    Xuyan Liu


    Full Text Available Based on an analysis of connotation and extension of the concept of the orthogonal curvilinear coordinates, we have deduced a platform of strain tensor expression of Cartesian coordinates, which turns out to be a function of Lame coefficient and unit vector. By using transform matrix between Cartesian coordinates and orthogonal curvilinear coordinates, we have deduced a mathematical expression for correcting displacement vector differential in orthogonal curvilinear coordinates, and given a general expression of strain tensor in orthogonal curvilinear coordinates.

  6. New discrete orthogonal moments for signal analysis

    Czech Academy of Sciences Publication Activity Database

    Honarvar Shakibaei Asli, Barmak; Flusser, Jan


    Roč. 141, č. 1 (2017), s. 57-73 ISSN 0165-1684 R&D Projects: GA ČR GA15-16928S Institutional support: RVO:67985556 Keywords : Orthogonal polynomials * Moment functions * Z-transform * Rodrigues formula * Hypergeometric form Subject RIV: JD - Computer Applications, Robotics Impact factor: 3.110, year: 2016 http:// library

  7. Rotation of 2D orthogonal polynomials

    Czech Academy of Sciences Publication Activity Database

    Yang, B.; Flusser, Jan; Kautský, J.


    Roč. 102, č. 1 (2018), s. 44-49 ISSN 0167-8655 R&D Projects: GA ČR GA15-16928S Institutional support: RVO:67985556 Keywords : Rotation invariants * Orthogonal polynomials * Recurrent relation * Hermite-like polynomials * Hermite moments Subject RIV: JD - Computer Applications, Robotics Impact factor: 1.995, year: 2016 http:// library

  8. Towards an Orthogonal Central Dogma (Preprint) (United States)


    expression. Synthetic biologists therefore write genetic programs with the host organism in mind and accept both the rigidities and regulatory...organism in mind and accept both the rigidities and regulatory complexities associated with host central dogma systems. This dependency creates two...Expanding and reprogramming the genetic code of cells and animals . Annu Rev Biochem 83, 379–408 (2014). 17. Wang, K. et al. Optimized orthogonal

  9. Direct energy functional minimization under orthogonality constraints (United States)

    Weber, Valéry; VandeVondele, Joost; Hutter, Jürg; Niklasson, Anders M. N.


    The direct energy functional minimization problem in electronic structure theory, where the single-particle orbitals are optimized under the constraint of orthogonality, is explored. We present an orbital transformation based on an efficient expansion of the inverse factorization of the overlap matrix that keeps orbitals orthonormal. The orbital transformation maps the orthogonality constrained energy functional to an approximate unconstrained functional, which is correct to some order in a neighborhood of an orthogonal but approximate solution. A conjugate gradient scheme can then be used to find the ground state orbitals from the minimization of a sequence of transformed unconstrained electronic energy functionals. The technique provides an efficient, robust, and numerically stable approach to direct total energy minimization in first principles electronic structure theory based on tight-binding, Hartree-Fock, or density functional theory. For sparse problems, where both the orbitals and the effective single-particle Hamiltonians have sparse matrix representations, the effort scales linearly with the number of basis functions N in each iteration. For problems where only the overlap and Hamiltonian matrices are sparse the computational cost scales as O(M2N ), where M is the number of occupied orbitals. We report a single point density functional energy calculation of a DNA decamer hydrated with 4003 water molecules under periodic boundary conditions. The DNA fragment containing a cis-syn thymine dimer is composed of 634 atoms and the whole system contains a total of 12 661 atoms and 103 333 spherical Gaussian basis functions.

  10. Chaperone binding at the ribosomal exit tunnel

    DEFF Research Database (Denmark)

    Kristensen, Ole; Gajhede, Michael


    The exit tunnel region of the ribosome is well established as a focal point for interaction between the components that guide the fate of nascent polypeptides. One of these, the chaperone trigger factor (TF), associates with the 50S ribosomal subunit through its N-terminal domain. Targeting of TF...

  11. Ribosome evolution: Emergence of peptide synthesis machinery

    Indian Academy of Sciences (India)

    remains unclear and many studies need to be performed. However, the crystal structure of the large ribosomal subunit of. Deinococcus ... radiodurans.rrnC.pdf/) (Cannone et al. 2002; Doshi et al. 2004). The following modifications were ... experimentally in future studies. In the evolutionary process from proto-ribosomes to.

  12. Structural view on recycling of archaeal and eukaryotic ribosomes after canonical termination and ribosome rescue. (United States)

    Franckenberg, Sibylle; Becker, Thomas; Beckmann, Roland


    Ribosome recycling usually occurs after canonical termination triggered by a stop codon. Additionally, ribosomes that are stalled by aberrant mRNAs need to be recognized and subsequently recycled. In eukaryotes and archaea, the factors involved in canonical termination and ribosome rescue are structurally and functionally related. Both termination and ribosome rescue are mediated by class I release factors (eRF1/aRF1 in eukaryotic/archaeal termination) or their paralogs (Pelota/aPelota for ribosome rescue) and homologs of translational GTPases (eRF3/aEF1α in termination, Hbs1/aEF1α in ribosome rescue). These events are followed by recycling of the ribosome. Recently the ATPase ABCE1 was shown to be the main ribosome recycling factor. In concert with eRF1 or Pelota, ABCE1 dissociates the ribosome into subunits. During the past two years, several structures of ribosome rescue and ribosome recycling complexes have been solved by cryo-electron microscopy and crystallography. These structures along with recent functional data make it possible to propose a molecular model of these late translation events in termination and recycling. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Analysis of ribosome biogenesis factor-modules in yeast cells depleted from pre-ribosomes. (United States)

    Merl, Juliane; Jakob, Steffen; Ridinger, Katrin; Hierlmeier, Thomas; Deutzmann, Rainer; Milkereit, Philipp; Tschochner, Herbert


    Formation of eukaryotic ribosomes requires more than 150 biogenesis factors which transiently interact with the nascent ribosomal subunits. Previously, many pre-ribosomal intermediates could be distinguished by their protein composition and rRNA precursor (pre-rRNA) content. We purified complexes of ribosome biogenesis factors from yeast cells in which de novo synthesis of rRNA precursors was down-regulated by genetic means. We compared the protein composition of these largely pre-rRNA free assemblies with the one of analogous pre-ribosomal preparations by semi-quantitative mass spectrometry. The experimental setup minimizes the possibility that the analysed pre-rRNA free protein modules were derived from (partially) disrupted pre-ribosomal particles and provides thereby strong evidence for their pre-ribosome independent existence. In support of the validity of this approach (i) the predicted composition of the analysed protein modules was in agreement with previously described rRNA-free complexes and (ii) in most of the cases we could identify new candidate members of reported protein modules. An unexpected outcome of these analyses was that free large ribosomal subunits are associated with a specific set of ribosome biogenesis factors in cells where neo-production of nascent ribosomes was blocked. The data presented strengthen the idea that assembly of eukaryotic pre-ribosomal particles can result from transient association of distinct building blocks.

  14. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. (United States)

    Jewett, Michael C; Fritz, Brian R; Timmerman, Laura E; Church, George M


    Purely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties.

  15. Differential Stoichiometry among Core Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Nikolai Slavov


    Full Text Available Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its dysregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs, some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.

  16. Differential Stoichiometry among Core Ribosomal Proteins (United States)

    Slavov, Nikolai; Semrau, Stefan; Airoldi, Edoardo; Budnik, Bogdan; van Oudenaarden, Alexander


    Summary Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its dysregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs), some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC) and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function. PMID:26565899

  17. A Dual Orthogonality Procedure for Nonlinear Finite Element Equations

    DEFF Research Database (Denmark)

    Krenk, S.; Hededal, O.

    In the orthogonal residual procedure for solution of nonlinear finite element equations the load is adjusted in each equilibrium iteration to satisfy an orthogonality condition to the current displacement increment. It is here shown that the quasi-newton formulation of the orthogonal residual...... method consists of a simple one-term correction of the displacement subincrement, and that this correction leads to orthogonality between the corrected displacement subincrement and the current increment of the internal force vector, thus defining a dual orthogonality algorithm. It is demonstrated how...

  18. Mentoring: An Evolving Relationship. (United States)

    Block, Michelle; Florczak, Kristine L


    The column concerns itself with mentoring as an evolving relationship between mentor and mentee. The collegiate mentoring model, the transformational transcendence model, and the humanbecoming mentoring model are considered in light of a dialogue with mentors at a Midwest university and conclusions are drawn.

  19. Measurably evolving populations

    DEFF Research Database (Denmark)

    Drummond, Alexei James; Pybus, Oliver George; Rambaut, Andrew


    processes through time. Populations for which such studies are possible � measurably evolving populations (MEPs) � are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through...... understanding of evolutionary processes in diverse organisms, from viruses to vertebrates....

  20. Eukaryote-specific rRNA expansion segments function in ribosome biogenesis. (United States)

    Ramesh, Madhumitha; Woolford, John L


    The secondary structure of ribosomal RNA (rRNA) is largely conserved across all kingdoms of life. However, eukaryotes have evolved extra blocks of rRNA sequences, relative to those of prokaryotes, called expansion segments (ES). A thorough characterization of the potential roles of ES remains to be done, possibly because of limitations in the availability of robust systems to study rRNA mutants. We sought to systematically investigate the potential functions, if any, of the ES in 25S rRNA of Saccharomyces cerevisiae by deletion mutagenesis. We deleted 14 of the 16 different eukaryote-specific ES in yeast 25S rRNA individually and assayed their phenotypes. Our results show that all but two of the ES tested are necessary for optimal growth and are required for production of 25S rRNA, suggesting that ES play roles in ribosome biogenesis. Further, we classified expansion segments into groups that participate in early nucleolar, middle, and late nucleoplasmic steps of ribosome biogenesis, by assaying their pre-rRNA processing phenotypes. This study is the first of its kind to systematically identify the functions of eukaryote-specific expansion segments by showing that they play roles in specific steps of ribosome biogenesis. The catalog of phenotypes we identified, combined with previous investigations of the roles ribosomal proteins in large subunit biogenesis, leads us to infer that assembling ribosomes are composed of distinct RNA and protein structural neighborhood clusters that participate in specific steps of ribosome biogenesis. © 2016 Ramesh and Woolford; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  1. Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides. (United States)

    Cromm, Philipp M; Schaubach, Sebastian; Spiegel, Jochen; Fürstner, Alois; Grossmann, Tom N; Waldmann, Herbert


    Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets.

  2. EVOLVE 2014 International Conference

    CERN Document Server

    Tantar, Emilia; Sun, Jian-Qiao; Zhang, Wei; Ding, Qian; Schütze, Oliver; Emmerich, Michael; Legrand, Pierrick; Moral, Pierre; Coello, Carlos


    This volume encloses research articles that were presented at the EVOLVE 2014 International Conference in Beijing, China, July 1–4, 2014.The book gathers contributions that emerged from the conference tracks, ranging from probability to set oriented numerics and evolutionary computation; all complemented by the bridging purpose of the conference, e.g. Complex Networks and Landscape Analysis, or by the more application oriented perspective. The novelty of the volume, when considering the EVOLVE series, comes from targeting also the practitioner’s view. This is supported by the Machine Learning Applied to Networks and Practical Aspects of Evolutionary Algorithms tracks, providing surveys on new application areas, as in the networking area and useful insights in the development of evolutionary techniques, from a practitioner’s perspective. Complementary to these directions, the conference tracks supporting the volume, follow on the individual advancements of the subareas constituting the scope of the confe...

  3. Evolvable Neural Software System (United States)

    Curtis, Steven A.


    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  4. Geometric reconstruction of biological orthogonal plywoods. (United States)

    Aguilar Gutierrez, Oscar F; Rey, Alejandro D


    In this paper we focus on the structural determination of biological orthogonal plywoods, fiber-like composite analogues of liquid crystalline phases, where the fibrils of the building blocks show sharp 90° orientation jumps between fibers in adjacent domains. We present an original geometric and computational modelling that allows us to determine the fibrillary orientation in biological plywoods from periodic herringbone patterns commonly observed in cross-sections. Although herringbone patterns were long reported, the specific and quantitative relationships between herringbones and the orthogonal plywoods were absent or at best incomplete. Here we provide an efficient and new procedure to perform an inverse problem that connects two specific features of the herringbone patterns (aperture angle and wavelength) with the 3D morphology of the structure, whose accuracy and validity were ascertained through in silico simulations and also with real specimens ("Eremosphaera viridis"). This contribution extends significantly the better known characterization methods of 2D cross sections, such as the arced patterns observed in biological helicoidal plywoods, and with the present proposed methodology it adds another characterization tool for a variety of biological fibrous composites that form cornea-like tissues.

  5. Is The Ribosome Targeted By Adaptive Mutations

    DEFF Research Database (Denmark)

    Jimenez Fernandez, Alicia; Molin, Søren; Johansen, Helle Krogh


    degree of evolutionary conservation of the cellular MMSM tend to support this view. However, under certain selective conditions the machinery itself may be targeted by adaptive mutations, which result in fitness-increasing phenotypic changes. Here we investigate and characterize the role of ribosomal...... mutations in adaptive evolution. Methods: Several mutations in ribosomal genes have been identified in the genome analysis of nearly 700 Pseudomonas aeruginosa isolates from infected cystic fibrosis patients. Among these mutations we have repeatedly identified insertions, deletions and substitutions...... in specific ribosomal genes. The bacterial phenotypes of the mutated strains will be investigated. Results: Preliminary assays show that mutant strains have reduced growth rate and an altered antibiotic resistance pattern. The selection for mutations in ribosomal protein genes is partly explainable...

  6. Implications of electrostatic potentials on ribosomal proteins. (United States)

    Kliber, J S; Hoa, G H; Douzou, P; Graffe, M; Grunberg-Manago, M


    Potentiometric studies of ribosomal particles 30S, 50S, and 70S, were designed to investigate possible implications of the electrostatic potentials developed by the 16S and 23S rRNA fractions. Release of protons and proton titrations of these ribosomal fractions were examined as a function of Mg2+ and K+ concentrations. The effects of these cations fit the polyelectrolyte theory remarkably well and are discussed accordingly. PMID:12498

  7. Structure of the human 80S ribosome. (United States)

    Khatter, Heena; Myasnikov, Alexander G; Natchiar, S Kundhavai; Klaholz, Bruno P


    Ribosomes are translational machineries that catalyse protein synthesis. Ribosome structures from various species are known at the atomic level, but obtaining the structure of the human ribosome has remained a challenge; efforts to address this would be highly relevant with regard to human diseases. Here we report the near-atomic structure of the human ribosome derived from high-resolution single-particle cryo-electron microscopy and atomic model building. The structure has an average resolution of 3.6 Å, reaching 2.9 Å resolution in the most stable regions. It provides unprecedented insights into ribosomal RNA entities and amino acid side chains, notably of the transfer RNA binding sites and specific molecular interactions with the exit site tRNA. It reveals atomic details of the subunit interface, which is seen to remodel strongly upon rotational movements of the ribosomal subunits. Furthermore, the structure paves the way for analysing antibiotic side effects and diseases associated with deregulated protein synthesis.

  8. Microtubule-dependent ribosome localization in C. elegans neurons (United States)

    Noma, Kentaro; Goncharov, Alexandr; Ellisman, Mark H


    Subcellular localization of ribosomes defines the location and capacity for protein synthesis. Methods for in vivo visualizing ribosomes in multicellular organisms are desirable in mechanistic investigations of the cell biology of ribosome dynamics. Here, we developed an approach using split GFP for tissue-specific visualization of ribosomes in Caenorhabditis elegans. Labeled ribosomes are detected as fluorescent puncta in the axons and synaptic terminals of specific neuron types, correlating with ribosome distribution at the ultrastructural level. We found that axonal ribosomes change localization during neuronal development and after axonal injury. By examining mutants affecting axonal trafficking and performing a forward genetic screen, we showed that the microtubule cytoskeleton and the JIP3 protein UNC-16 exert distinct effects on localization of axonal and somatic ribosomes. Our data demonstrate the utility of tissue-specific visualization of ribosomes in vivo, and provide insight into the mechanisms of active regulation of ribosome localization in neurons. PMID:28767038

  9. Regolith Evolved Gas Analyzer (United States)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug


    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  10. The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. (United States)

    Root-Bernstein, Robert; Root-Bernstein, Meredith


    We have proposed that the ribosome may represent a missing link between prebiotic chemistries and the first cells. One of the predictions that follows from this hypothesis, which we test here, is that ribosomal RNA (rRNA) must have encoded the proteins necessary for ribosomal function. In other words, the rRNA also functioned pre-biotically as mRNA. Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a "null" hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein. Five types of evidence reported here support the plausibility of the hypothesis that the mRNA encoding rb-proteins evolved from rRNA: (1) the ubiquity of rb-protein binding to their own mRNAs and autogenous control of their own translation; (2) the higher-than-expected incidence of Arginine-rich modules associated with RNA binding that occurs in rRNA-encoded proteins; (3) the fact that rRNA-binding regions of rb-proteins are homologous to their mRNA binding regions; (4) the higher than expected incidence of rb-protein sequences encoded in rRNA that are of a high degree of homology to their mRNA as compared with a random selection of other proteins; and (5) rRNA in modern prokaryotes and eukaryotes encodes functional proteins. None of these results can be explained by the null hypothesis that assumes independent evolution of rRNA and the mRNAs encoding ribosomal proteins. Also noteworthy is that very few proteins bind their own mRNAs that are not associated with ribosome function. Further tests of the hypothesis are suggested: (1) experimental testing of whether rRNA-encoded proteins bind to rRNA at their coding sites; (2) whether tRNA synthetases, which are also known to bind to their

  11. Application of eigenfunction orthogonalities to vibration problems

    CSIR Research Space (South Africa)

    Fedotov, I


    Full Text Available II WCE 2009, July 1 - 3, 2009, London, U.K. ISBN:978-988-18210-1-0 WCE 2009 the variation of the action ∫= 2 1 t t LdtS must be equal to zero for all 1t and 2t . [5]. Thus ∫ == 2 1 0 t t LdtS δδ (2) (It... ′ ′ + + = ∫ where ).1()0()( 21 2 0 1 0 22 2 nn yydxxyy nn αα ++′= ∫ (18) Proceedings of the World Congress on Engineering 2009 Vol II WCE 2009, July 1 - 3, 2009, London, U.K. ISBN:978-988-18210-1-0 WCE 2009 In the case α₀ = 1α =0 orthogonality...

  12. Partially orthogonal resonators for magnetic resonance imaging (United States)

    Chacon-Caldera, Jorge; Malzacher, Matthias; Schad, Lothar R.


    Resonators for signal reception in magnetic resonance are traditionally planar to restrict coil material and avoid coil losses. Here, we present a novel concept to model resonators partially in a plane with maximum sensitivity to the magnetic resonance signal and partially in an orthogonal plane with reduced signal sensitivity. Thus, properties of individual elements in coil arrays can be modified to optimize physical planar space and increase the sensitivity of the overall array. A particular case of the concept is implemented to decrease H-field destructive interferences in planar concentric in-phase arrays. An increase in signal to noise ratio of approximately 20% was achieved with two resonators placed over approximately the same planar area compared to common approaches at a target depth of 10 cm at 3 Tesla. Improved parallel imaging performance of this configuration is also demonstrated. The concept can be further used to increase coil density.

  13. Inverse solutions for tilting orthogonal double prisms. (United States)

    Li, Anhu; Ding, Ye; Bian, Yongming; Liu, Liren


    An analytical reverse solution and actual examples are given to show how to direct a laser beam from a pair of orthogonal prisms to given targets in free space. Considering the influences of double-prism structural parameters, a lookup table method to seek the numerical reverse solution of each prism's tilting angle is also proposed for steering the double-prism orientation to track a target position located in the near field. Some case studies, as well as a specified elliptical target trajectory scanned by the cam-based driving double prisms, exhibit the significant application values of the theoretical derivation. The analytic reverse and numerical solutions can be generalized to investigate the synthesis of scanning patterns and the controlling strategy of double-prism tilting motion, the potentials of which can be explored to perform the orientation and position tracking functions in applications of precision engineering fields.

  14. Saccharomyces cerevisiae Ribosomal Protein L26 Is Not Essential for Ribosome Assembly and Function (United States)

    Babiano, Reyes; Gamalinda, Michael


    Ribosomal proteins play important roles in ribosome biogenesis and function. Here, we study the evolutionarily conserved L26 in Saccharomyces cerevisiae, which assembles into pre-60S ribosomal particles in the nucle(ol)us. Yeast L26 is one of the many ribosomal proteins encoded by two functional genes. We have disrupted both genes; surprisingly, the growth of the resulting rpl26 null mutant is apparently identical to that of the isogenic wild-type strain. The absence of L26 minimally alters 60S ribosomal subunit biogenesis. Polysome analysis revealed the appearance of half-mers. Analysis of pre-rRNA processing indicated that L26 is mainly required to optimize 27S pre-rRNA maturation, without which the release of pre-60S particles from the nucle(ol)us is partially impaired. Ribosomes lacking L26 exhibit differential reactivity to dimethylsulfate in domain I of 25S/5.8S rRNAs but apparently are able to support translation in vivo with wild-type accuracy. The bacterial homologue of yeast L26, L24, is a primary rRNA binding protein required for 50S ribosomal subunit assembly in vitro and in vivo. Our results underscore potential differences between prokaryotic and eukaryotic ribosome assembly. We discuss the reasons why yeast L26 plays such an apparently nonessential role in the cell. PMID:22688513

  15. Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features. (United States)

    Shasmal, Manidip; Sengupta, Jayati


    Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.

  16. Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding (United States)

    Sharma, Ajeet K.; Chowdhury, Debashish


    Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechanochemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Wherever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.

  17. Precursors of ribosomal RNA in yeast nucleus : Biosynthesis and relation to cytoplasmic ribosomal RNA

    NARCIS (Netherlands)

    Sillevis Smitt, W.W.; Vlak, J.M.; Schiphof, R.; Rozijn, Th.H.

    In vivo methylated precursors of ribosomal RNA in yeast have been characterized on acrylamide gels. The initial ribosomal precursor in the yeast nucleus is a 37S RNA component, which is processed to a nuclear 28S RNA. Both the 37S and the 28S RNA components are important constituents of the yeast

  18. Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity (United States)

    Xie, Ping


    The performance of ribosome translation can be characterized by two factors, the translation rate and fidelity. Here, we provide analytical studies of the effect of the near-cognate tRNAs on the two factors. It is shown that the increase of the concentration of the near-cognate tRNAs relative to that of the cognate tRNA has negative effects on the ribosome translation by reducing both the translation rate and the translation fidelity. The effect of the near-cognate ternary complexes on the translation rate results mainly from the initial selection phase, whereas the proofreading phase has a minor effect. By contrast, the effect of the near-cognate ternary complexes on the fidelity results almost equally from the two phases. By using two successive phases, the initial selection and the proofreading, the ribosome can achieve higher translation fidelity than the product of the fidelity when only the initial selection is included and when only the proofreading is included, especially at the large ratio of the concentration of the near-cognate tRNAs compared to that of the cognate tRNA. Moreover, we study the changes of the free energy landscape in the tRNA decoding step. It is found that the rate constants of the tRNA decoding step measured experimentally give the minimum energy changes for the ribosomal complex to attain the optimal performance with both the highest decoding rate and fidelity and/or with the maximum value of the decoding fitness function. This suggests that the ribosome has evolved to utilize the minimum free energy changes gained from the conformational changes of the ribosome, EF-Tu, and tRNA to achieve the optimal performance in the tRNA decoding.

  19. Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya. (United States)

    Benelli, Dario; Marzi, Stefano; Mancone, Carmine; Alonzi, Tonino; la Teana, Anna; Londei, Paola


    The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal-eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.

  20. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. (United States)

    Zhang, Yanqing; Mandava, Chandra Sekhar; Cao, Wei; Li, Xiaojing; Zhang, Dejiu; Li, Ningning; Zhang, Yixiao; Zhang, Xiaoxiao; Qin, Yan; Mi, Kaixia; Lei, Jianlin; Sanyal, Suparna; Gao, Ning


    Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.

  1. The ribosome can prevent aggregation of partially folded protein intermediates: studies using the Escherichia coli ribosome.

    Directory of Open Access Journals (Sweden)

    Bani Kumar Pathak

    Full Text Available BACKGROUND: Molecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone 'foldases' that are distinct from chaperone' holdases' that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains. RESULTS: We demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein. CONCLUSION: The ribosome can behave like a 'holdase' chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.

  2. Functional Importance of Mobile Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Kai-Chun Chang


    Full Text Available Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins, whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.

  3. Programmed evolution for optimization of orthogonal metabolic output in bacteria.

    Directory of Open Access Journals (Sweden)

    Todd T Eckdahl

    Full Text Available Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in

  4. Orthogonal Matching Pursuit under the Restricted Isometry Property (United States)


    We refer the reader to the survey article [6] as a general reference. Our particular interest is in understanding what properties of the dictionary...1.7) where Pk is the orthogonal projector onto Fk. OMP is also called the Orthogonal Greedy Algorithm. More generally, we analyze the Weak

  5. Processing of dual-orthogonal cw polarimetric radar signals

    NARCIS (Netherlands)

    Babur, G.


    The thesis consists of two parts. The first part is devoted to the theory of dual-orthogonal polarimetric radar signals with continuous waveforms. The thesis presents a comparison of the signal compression techniques, namely correlation and de-ramping methods, for the dual-orthogonal sophisticated

  6. Frequency dependence of orthogonal polarisation modes in pulsars

    NARCIS (Netherlands)

    Smits, J.M.; Stappers, B.W.; Edwards, R.T.; Kuijpers, J.; Ramachandran, R.


    We have carried out a study of the orthogonal polarisation mode behaviour as afunction of frequency of 18pulsars, using average pulsar data from the European Pulsar Network(EPN). Assuming that the radiation consists of two100% polarised completely orthogonal superposed modes we separated these

  7. Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3' untranslated regions. (United States)

    Miettinen, Teemu P; Björklund, Mikael


    Ribosome profiling identifies ribosome positions on translated mRNAs. A prominent feature of published datasets is the near complete absence of ribosomes in 3' untranslated regions (3'UTR) although substantial ribosome density can be observed on non-coding RNAs. Here we perform ribosome profiling in cultured Drosophila and human cells and show that different features of translation are revealed depending on the nuclease and the digestion conditions used. Most importantly, we observe high abundance of ribosome protected fragments in 3'UTRs of thousands of genes without manipulation of translation termination. Affinity purification of ribosomes indicates that the 3'UTR reads originate from ribosome protected fragments. Association of ribosomes with the 3'UTR may be due to ribosome migration through the stop codon or 3'UTR mRNA binding to ribosomes on the coding sequence. This association depends primarily on the relative length of the 3'UTR and may be related to translational regulation or ribosome recycling, for which the efficiency is known to inversely correlate with 3'UTR length. Together our results indicate that ribosome profiling is highly dependent on digestion conditions and that ribosomes commonly associate with the 3'UTR, which may have a role in translational regulation. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions (United States)

    Miettinen, Teemu P.; Björklund, Mikael


    Ribosome profiling identifies ribosome positions on translated mRNAs. A prominent feature of published datasets is the near complete absence of ribosomes in 3′ untranslated regions (3′UTR) although substantial ribosome density can be observed on non-coding RNAs. Here we perform ribosome profiling in cultured Drosophila and human cells and show that different features of translation are revealed depending on the nuclease and the digestion conditions used. Most importantly, we observe high abundance of ribosome protected fragments in 3′UTRs of thousands of genes without manipulation of translation termination. Affinity purification of ribosomes indicates that the 3′UTR reads originate from ribosome protected fragments. Association of ribosomes with the 3′UTR may be due to ribosome migration through the stop codon or 3′UTR mRNA binding to ribosomes on the coding sequence. This association depends primarily on the relative length of the 3′UTR and may be related to translational regulation or ribosome recycling, for which the efficiency is known to inversely correlate with 3′UTR length. Together our results indicate that ribosome profiling is highly dependent on digestion conditions and that ribosomes commonly associate with the 3′UTR, which may have a role in translational regulation. PMID:25550424

  9. The Design of the Orthogonal Box Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Moretti, Alfred; /Fermilab


    The muon collider and/or the neutrino factory require large accelerating electric field gradients immersed in large (3 to 6 T) solenoidal magnetic fields for ionization cooling of muon beams. Our original vacuum breakdown study demonstrated a loss of achievable peak accelerating gradient in solenoidal magnetic fields by a factor 2 or greater. The Muon Collaboration has developed a theory of a method to suppress high electric field breakdown in vacuum cavities needed for a Muon collider or neutrino factory. It has been shown in our studies and by others that high gradient electric field emitted electrons (dark current) are the primary cause of breakdown. A DC magnetic field orthogonal to the RF electric accelerating field prevents dark current high field emitted electrons from traveling across the accelerating gap and then will prevent breakdown. We have decided to test this theory by building a special cavity in the shape of vacuum box. Figure 1 is a simplified view of the cavity design. The design is based on an 805 MHz WR975 waveguide cavity resonating in the TE{sub 101} mode. For the TE{sub 101} mode the resonant frequency f{sub 0} is given by the relationship f{sub 0} = c[(I/a){sup 2} + (m/b){sup 2} + (n/d){sup 2}]{sup 0.5}/2 where a and d are the lengths of the base sides and b is the height of the box in MKS units and c is the velocity of light.

  10. Surface-attached orthogonal gradient hydrogels (United States)

    Chinnayan Kannan, Pandiyarajan; Genzer, Jan

    Gradient materials play a significant role in the creation of artificial implants due to their potential to reduce stress concentration when two or more structures with different mechanical properties are joined together, e . g . , tendon, a fibrous protein that connects the soft and hard muscle tissues in our body. We employ free radical polymerization to synthesize random copolymers containing 90% of N-isopropyl acrylamide (NIPAAm), 5% photo-active methacrylyloxybenzophenone (MABP) and 5% thermally-active styrenesulfonylazide (SSAz) crosslinkers. The presence of MABP and SSAz facilitates adjusting gel density on a flat support in two orthogonal directions by spatially and independently controlling UV dosage and temperature. The swelling behavior (α) of the gels in water and methanol is examined using a spectroscopic ellipsometry and the degree of swelling depends on the extent of crosslinking that ranges from α = 1-1.2 (highly crosslinked gels) to α = 4-5 (loosely crosslinked gels). We compare the network properties surface-attached gels and un-attached identical counterparts and confirm that the linear swelling ratio of surface-attached networks is higher than that of the corresponding un-attached gels.

  11. Orthogonal protein decoration of DNA nanostructures. (United States)

    Meyer, Rebecca; Niemeyer, Christof M


    The development of robust DNA-protein coupling techniques is mandatory for applications of DNA nanostructures in biomedical diagnostics, fundamental biochemistry, and other fields in biomolecular nanosciences. The use of self-labeling fusion proteins, which are orthogonal to biotin-streptavidin and antibody-antigen interactions, is described for the site-selective protein decoration of two exemplary DNA nanostructures: a four-way junction X-tile motif and a 3D DNA tetrahedron. Multifunctional DNA superstructures bearing up to four different proteins are generated and characterized by electrophoresis and microplate-based functionality assays. Steric and electrostatic interactions are identified as critical parameters controlling the efficiency of DNA-protein ligation. The results indicate that this method is versatile and broadly applicable, not only for the functionalization of DNA architectures but also for the site-specific decoration of other molecular materials and devices containing several different proteins. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Fat: an evolving issue

    Directory of Open Access Journals (Sweden)

    John R. Speakman


    Work on obesity is evolving, and obesity is a consequence of our evolutionary history. In the space of 50 years, we have become an obese species. The reasons why can be addressed at a number of different levels. These include separating between whether the primary cause lies on the food intake or energy expenditure side of the energy balance equation, and determining how genetic and environmental effects contribute to weight variation between individuals. Opinion on whether increased food intake or decreased energy expenditure drives the obesity epidemic is still divided, but recent evidence favours the idea that food intake, rather than altered expenditure, is most important. There is more of a consensus that genetics explains most (probably around 65% of weight variation between individuals. Recent advances in genome-wide association studies have identified many polymorphisms that are linked to obesity, yet much of the genetic variance remains unexplained. Finding the causes of this unexplained variation will be an impetus of genetic and epigenetic research on obesity over the next decade. Many environmental factors – including gut microbiota, stress and endocrine disruptors – have been linked to the risk of developing obesity. A better understanding of gene-by-environment interactions will also be key to understanding obesity in the years to come.

  13. Evolving Concepts of Asthma (United States)

    Ray, Anuradha; Wenzel, Sally E.


    Our understanding of asthma has evolved over time from a singular disease to a complex of various phenotypes, with varied natural histories, physiologies, and responses to treatment. Early therapies treated most patients with asthma similarly, with bronchodilators and corticosteroids, but these therapies had varying degrees of success. Similarly, despite initial studies that identified an underlying type 2 inflammation in the airways of patients with asthma, biologic therapies targeted toward these type 2 pathways were unsuccessful in all patients. These observations led to increased interest in phenotyping asthma. Clinical approaches, both biased and later unbiased/statistical approaches to large asthma patient cohorts, identified a variety of patient characteristics, but they also consistently identified the importance of age of onset of disease and the presence of eosinophils in determining clinically relevant phenotypes. These paralleled molecular approaches to phenotyping that developed an understanding that not all patients share a type 2 inflammatory pattern. Using biomarkers to select patients with type 2 inflammation, repeated trials of biologics directed toward type 2 cytokine pathways saw newfound success, confirming the importance of phenotyping in asthma. Further research is needed to clarify additional clinical and molecular phenotypes, validate predictive biomarkers, and identify new areas for possible interventions. PMID:26161792

  14. Evolving endoscopic surgery. (United States)

    Sakai, Paulo; Faintuch, Joel


    Since the days of Albukasim in medieval Spain, natural orifices have been regarded not only as a rather repugnant source of bodily odors, fluids and excreta, but also as a convenient invitation to explore and treat the inner passages of the organism. However, surgical ingenuity needed to be matched by appropriate tools and devices. Lack of technologically advanced instrumentation was a strong deterrent during almost a millennium until recent decades when a quantum jump materialized. Endoscopic surgery is currently a vibrant and growing subspecialty, which successfully handles millions of patients every year. Additional opportunities lie ahead which might benefit millions more, however, requiring even more sophisticated apparatuses, particularly in the field of robotics, artificial intelligence, and tissue repair (surgical suturing). This is a particularly exciting and worthwhile challenge, namely of larger and safer endoscopic interventions, followed by seamless and scarless recovery. In synthesis, the future is widely open for those who use together intelligence and creativity to develop new prototypes, new accessories and new techniques. Yet there are many challenges in the path of endoscopic surgery. In this new era of robotic endoscopy, one will likely need a virtual simulator to train and assess the performance of younger doctors. More evidence will be essential in multiple evolving fields, particularly to elucidate whether more ambitious and complex pathways, such as intrathoracic and intraperitoneal surgery via natural orifice transluminal endoscopic surgery (NOTES), are superior or not to conventional techniques. © 2014 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  15. Asymmetric evolving random networks (United States)

    Coulomb, S.; Bauer, M.


    We generalize the Poissonian evolving random graph model of M. Bauer and D. Bernard (2003), to deal with arbitrary degree distributions. The motivation comes from biological networks, which are well-known to exhibit non Poissonian degree distributions. A node is added at each time step and is connected to the rest of the graph by oriented edges emerging from older nodes. This leads to a statistical asymmetry between incoming and outgoing edges. The law for the number of new edges at each time step is fixed but arbitrary. Thermodynamical behavior is expected when this law has a large time limit. Although (by construction) the incoming degree distributions depend on this law, this is not the case for most qualitative features concerning the size distribution of connected components, as long as the law has a finite variance. As the variance grows above 1/4, the average being < 1/2, a giant component emerges, which connects a finite fraction of the vertices. Below this threshold, the distribution of component sizes decreases algebraically with a continuously varying exponent. The transition is of infinite order, in sharp contrast with the case of static graphs. The local-in-time profiles for the components of finite size allow to give a refined description of the system.

  16. Evolving a photosynthetic organelle

    Directory of Open Access Journals (Sweden)

    Nakayama Takuro


    Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  17. Dom34 Rescues Ribosomes in 3´ Untranslated Regions (United States)

    Guydosh, Nicholas R.; Green, Rachel


    SUMMARY Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here we extend ribosome profiling methodology to reveal a high-resolution molecular characterization of Dom34 function in vivo. Dom34 removes stalled ribosomes from truncated mRNAs, but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3´ UTRs. These ribosomes appear to gain access to the 3 UTR via a mechanism that does not require decoding of the mRNA. These results suggest that ribosomes frequently enter downstream noncoding regions and that Dom34 carries out the important task of rescuing them. PMID:24581494

  18. Ribosomes Dance to a Daily Rhythm. (United States)

    Iyer, Aishwarya; Grummt, Ingrid


    Sinturel et al. demonstrate that feeding-fasting rhythms and light-dark cycles direct daily changes in liver mass and cell size. These feeding-fasting- and light-dark-driven diurnal fluctuations are controlled by an unconventional mechanism that affects ribosome assembly and protein levels during the active phase. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Modeling Interactions of Erythromycin Derivatives with Ribosomes. (United States)

    Shishkina, A V; Makarova, T M; Tereshchenkov, A G; Makarov, G I; Korshunova, G A; Bogdanov, A A


    Using a method of static simulation, a series of erythromycin A analogs was designed with aldehyde functions introduced instead of one of the methyl substituents in the 3'-N-position of the antibiotic that was potentially capable of forming a covalent bond with an amino group of one of the nucleotide residues of the 23S rRNA in the ribosomal exit tunnel. Similar interaction is observed for antibiotics of the tylosin series, which bind tightly to the large ribosomal subunit and demonstrate high antibacterial activity. Binding of novel erythromycin derivatives with the bacterial ribosome was investigated with the method of fluorescence polarization. It was found that the erythromycin analog containing a 1-methyl-3-oxopropyl group in the 3'-N-position demonstrates the best binding. Based on the ability to inhibit protein biosynthesis, it is on the same level as erythromycin, and it is significantly better than desmethyl-erythromycin. Molecular dynamic modeling of complexes of the derivatives with ribosomes was conducted to explain the observed effects.

  20. Ribosome display for improved biotherapeutic molecules. (United States)

    Rothe, Achim; Hosse, Ralf J; Power, Barbara E


    Ribosome display presents an innovative in vitro technology for the rapid isolation and evolution of high-affinity peptides or proteins. Displayed proteins are bound to and recovered from target molecules in multiple rounds of selection in order to enrich for specific binding proteins. No transformation step is necessary, which could lead to a loss of library diversity. A cycle of display and selection can be performed in one day, enabling the existing gene repertoire to be rapidly scanned. Proteins isolated from the panning rounds can be further modified through random or directed molecular evolution for affinity maturation, as well as selected for characteristics such as protein stability, folding and functional activity. Recently, the field of display technologies has become more prominent due to the generation of new scaffolds for ribosome display, isolation of high-affinity human antibodies by phage display, and their implementation in the discovery of novel protein-protein interactions. Applications for this technology extend into the broad field of antibody engineering, proteomics, and synthetic enzymes for diagnostics and therapeutics in cancer, autoimmune and infectious diseases, neurodegenerative diseases and inflammatory disorders. This review highlights the role of ribosome display in drug discovery, discusses advantages and disadvantages of the system, and attempts to predict the future impact of ribosome display technology on the development of novel engineered biopharmaceutical products for biological therapies.

  1. Evaluation of a ribosomal vaccine against pertussis. (United States)

    Field, L H; Parker, C D; Manclark, C R; Berry, L J


    A crude ribosomal vaccine derived from Bordetella pertussis administered to ICR and N:NIH (SW) strains of mice protected them effectively against a standardized intracranial challenge. The dose of vaccine that protected half the mice was less for N:NIH (SW) than for ICR mice and compared favorably with a killed reference vaccine. Ribosomes prepared from bacteria ground with washed sea sand were more immunogenic than those obtained by rupture with alumina or with a Braun homogenizer. The protective effect of the crude ribosomes was not an innate part of the organelle but was due to a substance or substances that could be removed from them by a 1 M NH4Cl wash. The material in the wash was highly immunogenic and retained both the histamine-sensitizing and leukocytosis-promoting properties. It lost much of the dermonecrotic activity and was poorly pyrogenic in rabbits. The most potent pyrogen was present in the washed ribosomes, which apparently, retained the endotoxic components of the cell wall. The best vaccines permitted acceptable weight gain in the immunized mice. PMID:222684

  2. Control of Ribosome Synthesis in Escherichia coli

    DEFF Research Database (Denmark)

    Molin, Søren; Meyenburg, K. von; Måløe, O.


    The rate of ribosome synthesis and accumulation in Escherichia coli during the transition after an energy source shift-down was analyzed. The shift was imposed on cultures of stringent and relaxed strains growing in glucose minimal medium by the addition of the glucose analogue {alpha...

  3. Diamond-Blackfan anemia, ribosome and erythropoiesis. (United States)

    Da Costa, L; Moniz, H; Simansour, M; Tchernia, G; Mohandas, N; Leblanc, T


    Diamond-Blackfan anemia is a rare inherited bone marrow failure syndrome (five to seven cases per million live births) characterized by an aregenerative, usually macrocytic anemia with an absence or less than 5% of erythroid precursors (erythroblastopenia) in an otherwise normal bone marrow. The platelet and the white cell counts are usually normal but neutropenia, thrombopenia or thrombocytosis have been noted at diagnosis. In 40 to 50% of DBA patients, congenital abnormalities mostly in the cephalic area and in thumbs and upper limbs have been described. Recent analysis did show a phenotype/genotype correlation. Congenital erythroblastopenia of DBA is the first human disease identified to result from defects in ribosomal biogenesis. The first ribosomal gene involved in DBA, ribosomal protein (RP) gene S19 (RPS19 gene), was identified in 1999. Subsequently, mutations in 12 other RP genes out of a total of 78 RP genes have been identified in DBA. All RP gene mutations described to date are heterozygous and dominant inheritance has been documented in 40 to 45% of affected individuals. As RP mutations are yet to be identified in approximately 50% of DBA cases, it is likely that other yet to be identified genes involved in ribosomal biogenesis or other pathways may be responsible for DBA phenotype. Copyright 2010 Elsevier Masson SAS. All rights reserved.

  4. Polar Plate Theory for Orthogonal Anisotropy (United States)

    Bailey, Michelle D.; Bower, Mark V.


    Laminated fiber-reinforced (or filamentary) composites are used today for their high strength-to-weight and stiffness-to-weight ratios. However, because of the anisotropic behavior of composites, determining the response on a macroscopic scale is challenging. This is particularly evident in the evaluation of the governing differential equations of a circular disk with the fibers of the lamina oriented with rectilinear orthogonality. This includes any situation involving a composite plate of circular geometry in which out-of-plane displacements due to load are desired, such as fastener pull through loading of a composite plate. Current analysis techniques use numerical methods with rectilinear coordinate systems to solve problems with circular geometry. These analyses over predict plate stiffness by 20% and underpredict failure by 70%. Consequently, there is a need to transform classical composite plate theory to a polar coordinate system. In order to better analyze structures with circular geometries the classical composite plate equations are transformed into the plate equations for a rectilinearly anisotropic composite in polar coordinates. A composite plate is typically a laminate of fibers in rectilinear directions. Subsequent to the lay-tip the necessary geometry is cut out of a rectangular plate. In a similar manner, the derivation of the plate equation starts with the fundamental definitions of strain, displacement and curvature and incorporates the material property angular dependence into the equilibrium equations for a differential polar element. In the transformed state, the stiffness coefficients are no longer constant, adding to the complexity of the governing differential equations. This paper discusses the new derivation and evaluation of the plate equations for a circular composite disk with orthogonal rectilinear anisotropy. The resultant new three partial differential equations, which describe the circular anisotropic plate, can be used to

  5. Hermitian Self-Orthogonal Constacyclic Codes over Finite Fields

    Directory of Open Access Journals (Sweden)

    Amita Sahni


    Full Text Available Necessary and sufficient conditions for the existence of Hermitian self-orthogonal constacyclic codes of length n over a finite field Fq2, n coprime to q, are found. The defining sets and corresponding generator polynomials of these codes are also characterised. A formula for the number of Hermitian self-orthogonal constacyclic codes of length n over a finite field Fq2 is obtained. Conditions for the existence of numerous MDS Hermitian self-orthogonal constacyclic codes are obtained. The defining set and the number of such MDS codes are also found.

  6. Skew-orthogonal polynomials, differential systems and random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Saugata [Abdus Salam ICTP, Strada Costiera 11, 34100, Trieste (Italy)


    We study skew-orthogonal polynomials with respect to the weight function exp [ - 2V(x)], with V(x) = {sigma}{sup 2d}{sub K=1}(u{sub K}/K)x{sup K}, u{sub 2d} > 0, d > 0. A finite subsequence of such skew-orthogonal polynomials arising in the study of orthogonal and symplectic ensembles of random matrices satisfies a system of differential-difference-deformation equation. The vectors formed by such subsequence have the rank equal to the degree of the potential in the quaternion sense. These solutions satisfy certain compatibility condition and hence admit a simultaneous fundamental system of solutions.

  7. Subjective ranking of concert halls substantiated through orthogonal objective parameters. (United States)

    Cerdá, Salvador; Giménez, Alicia; Cibrián, Rosa; Girón, Sara; Zamarreño, Teófilo


    This paper studies the global subjective assessment, obtained from mean values of the results of surveys addressed to members of the audience of live concerts in Spanish auditoriums, through the mean values of the three orthogonal objective parameters (Tmid, IACCE3, and LEV), expressed in just noticeable differences (JNDs), regarding the best-valued hall. Results show that a linear combination of the relative variations of orthogonal parameters can largely explain the overall perceived quality of the sample. However, the mean values of certain orthogonal parameters are not representative, which shows that an alternative approach to the problem is necessary. Various possibilities are proposed.

  8. Orthogonal polynomials on the unit circle part 2 spectral theory

    CERN Document Server

    Simon, Barry


    This two-part book is a comprehensive overview of the theory of probability measures on the unit circle, viewed especially in terms of the orthogonal polynomials defined by those measures. A major theme involves the connections between the Verblunsky coefficients (the coefficients of the recurrence equation for the orthogonal polynomials) and the measures, an analog of the spectral theory of one-dimensional Schrödinger operators. Among the topics discussed along the way are the asymptotics of Toeplitz determinants (Szegő's theorems), limit theorems for the density of the zeros of orthogonal po

  9. Orthogonal polynomials on the unit circle part 1 classical theory

    CERN Document Server


    This two-part book is a comprehensive overview of the theory of probability measures on the unit circle, viewed especially in terms of the orthogonal polynomials defined by those measures. A major theme involves the connections between the Verblunsky coefficients (the coefficients of the recurrence equation for the orthogonal polynomials) and the measures, an analog of the spectral theory of one-dimensional Schrodinger operators. Among the topics discussed along the way are the asymptotics of Toeplitz determinants (Szegő's theorems), limit theorems for the density of the zeros of orthogonal po

  10. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. (United States)

    Po, Pengse; Delaney, Erin; Gamper, Howard; Szantai-Kis, D Miklos; Speight, Lee; Tu, LiWei; Kosolapov, Andrey; Petersson, E James; Hou, Ya-Ming; Deutsch, Carol


    All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the life-sustaining tasks of faithfully decoding mRNA and catalyzing peptide bond formation at the peptidyl transferase center (PTC). The ribosome has evolved an exit tunnel to host the elongating new peptide, protect it from proteolytic digestion, and guide its emergence. It is here that the nascent chain begins to fold. This folding process depends on the rate of translation at the PTC. We report here that besides PTC events, translation kinetics depend on steric constraints on nascent peptide side chains and that confined movements of cramped side chains within and through the tunnel fine-tune elongation rates. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. The characterization of cytoplasmic ribosomal protein genes in ...

    African Journals Online (AJOL)

    Microsporidia are obligate intracellular, eukaryotic parasites of medical and commercial importance, which can infect almost all animals including humans. However, their ribosomes are not of the 80S type as other eukaryotes, but like the prokaryotic 70S ribosome. In order to get the global composition of ribosomal protein ...

  12. Presence of Two Sets of Ribosomal Genes in Phytopathogenic Mollicutes (United States)

    Schneider, B.; Seemüller, E.


    DNA from 28 strains of phytopathogenic mycoplasmalike organisms that represented five primary taxonomic clusters was digested with restriction endonucleases and hybridized with several ribosomal probes. The results indicate the presence of two sets of ribosomal genes in all strains examined. Restriction maps of the two ribosomal operons for a group of 12 aster yellows mycoplasmalike organisms were constructed. Images PMID:16349389

  13. Fast Orthogonal Row-Column Electronic Scanning With Top-Orthogonal-to-Bottom Electrode Arrays. (United States)

    Ceroici, Chris; Harrison, Tyler; Zemp, Roger J


    Recently, top-orthogonal-to-bottom electrode 2-D arrays were introduced as a practical design for 3-D ultrasound imaging without requiring the wiring of a 2-D grid of elements. However, previously proposed imaging schemes suffered from speed or image-quality limitations. Here, we propose a new imaging scheme which we call Fast Orthogonal Row-Column Electronic Scanning (FORCES). This new approach takes advantage of bias sensitivity to enable high-quality and fast B-scan imaging. We compare this imaging scheme with an equivalent linear array, a previously proposed row-column imaging scheme, as well as with the Explososcan imaging scheme for 2-D arrays through simulations. In a point phantom simulation, the lateral (azimuthal) resolution of a 64 ×64 element 6.67-MHz λ /2-pitch array using the FORCES imaging scheme with an f-number of 1.7 was 0.52 mm with similar in-plane image quality to an equivalent linear array but with improved and electronically steerable elevational resolution. When compared with other 3-D imaging schemes in point phantom simulations, the FORCES imaging scheme showed an azimuthal resolution improvement of 54% compared with Explososcan. Compared with a previously introduced row-column method, the FORCES imaging scheme had similar resolution but a 25-dB decrease in sidelobe amplitude, significantly impacting contrast to noise in scattering phantoms.

  14. Skew-orthogonal polynomials and random matrix theory

    CERN Document Server

    Ghosh, Saugata


    Orthogonal polynomials satisfy a three-term recursion relation irrespective of the weight function with respect to which they are defined. This gives a simple formula for the kernel function, known in the literature as the Christoffel-Darboux sum. The availability of asymptotic results of orthogonal polynomials and the simple structure of the Christoffel-Darboux sum make the study of unitary ensembles of random matrices relatively straightforward. In this book, the author develops the theory of skew-orthogonal polynomials and obtains recursion relations which, unlike orthogonal polynomials, depend on weight functions. After deriving reduced expressions, called the generalized Christoffel-Darboux formulas (GCD), he obtains universal correlation functions and non-universal level densities for a wide class of random matrix ensembles using the GCD. The author also shows that once questions about higher order effects are considered (questions that are relevant in different branches of physics and mathematics) the ...

  15. Systems of Differential Equations with Skew-Symmetric, Orthogonal Matrices (United States)

    Glaister, P.


    The solution of a system of linear, inhomogeneous differential equations is discussed. The particular class considered is where the coefficient matrix is skew-symmetric and orthogonal, and where the forcing terms are sinusoidal. More general matrices are also considered.

  16. Wireless Magnetic Sensor with Orthogonal Frequency Coding Project (United States)

    National Aeronautics and Space Administration — The goal of this SBIR Phase I research project is to develop batteryless, wireless magnetic sensors with orthogonal frequency coding (OFC). These sensors will be...

  17. Properties of Orthogonal Gaussian-Hermite Moments and Their Applications

    Directory of Open Access Journals (Sweden)

    Jun Shen


    Full Text Available Moments are widely used in pattern recognition, image processing, and computer vision and multiresolution analysis. In this paper, we first point out some properties of the orthogonal Gaussian-Hermite moments, and propose a new method to detect the moving objects by using the orthogonal Gaussian-Hermite moments. The experiment results are reported, which show the good performance of our method.

  18. Non-Orthogonal Opportunistic Beamforming: Performance Analysis and Implementation

    KAUST Repository

    Xia, Minghua


    Aiming to achieve the sum-rate capacity in multi-user multi-antenna systems where $N_t$ antennas are implemented at the transmitter, opportunistic beamforming (OBF) generates~$N_t$ orthonormal beams and serves $N_t$ users during each channel use, which results in high scheduling delay over the users, especially in densely populated networks. Non-orthogonal OBF with more than~$N_t$ transmit beams can be exploited to serve more users simultaneously and further decrease scheduling delay. However, the inter-beam interference will inevitably deteriorate the sum-rate. Therefore, there is a tradeoff between sum-rate and scheduling delay for non-orthogonal OBF. In this context, system performance and implementation of non-orthogonal OBF with $N>N_t$ beams are investigated in this paper. Specifically, it is analytically shown that non-orthogonal OBF is an interference-limited system as the number of users $K \\\\to \\\\infty$. When the inter-beam interference reaches its minimum for fixed $N_t$ and~$N$, the sum-rate scales as $N\\\\ln\\\\left(\\\\frac{N}{N-N_t}\\ ight)$ and it degrades monotonically with the number of beams $N$ for fixed $N_t$. On the contrary, the average scheduling delay is shown to scale as $\\\\frac{1}{N}K\\\\ln{K}$ channel uses and it improves monotonically with $N$. Furthermore, two practical non-orthogonal beamforming schemes are explicitly constructed and they are demonstrated to yield the minimum inter-beam interference for fixed $N_t$ and $N$. This study reveals that, if user traffic is light and one user can be successfully served within a single transmission, non-orthogonal OBF can be applied to obtain lower worst-case delay among the users. On the other hand, if user traffic is heavy, non-orthogonal OBF is inferior to orthogonal OBF in terms of sum-rate and packet delay.


    Directory of Open Access Journals (Sweden)



    Full Text Available In the stages of understanding and study, by students, of descriptive geometry, the treble orthogonal projection of a point, creates problems in the situations in that one or more descriptive coordinates are zero. Starting from these considerations the authors have created an original computer program which offers to the students the possibility to easily understanding of the way in which a point is represented, in draught, in the treble orthogonal projection whatever which are its values of the descriptive coordinates.

  20. Representations of the Schroedinger group and matrix orthogonal polynomials

    Energy Technology Data Exchange (ETDEWEB)

    Vinet, Luc [Centre de recherches mathematiques, Universite de Montreal, CP 6128, succ. Centre-ville, Montreal, QC H3C 3J7 (Canada); Zhedanov, Alexei, E-mail:, E-mail: [Donetsk Institute for Physics and Technology, Donetsk 83114 (Ukraine)


    The representations of the Schroedinger group in one space dimension are explicitly constructed in the basis of the harmonic oscillator states. These representations are seen to involve matrix orthogonal polynomials in a discrete variable that have Charlier and Meixner polynomials as building blocks. The underlying Lie-theoretic framework allows for a systematic derivation of the structural formulas (recurrence relations, difference equations, Rodrigues' formula, etc) that these matrix orthogonal polynomials satisfy. (paper)

  1. Layer-Optimized Streaming of Motion-Compensated Orthogonal Video


    SHEN, Wenjie


    This report presents a layer-optimized streaming technique for delivering video content over the Internet using quality-scalable motion-compensated orthogonal video. We use Motion-Compensated Orthogonal Transforms (MCOT) to remove temporal and spatial redundancy. The resulting subbands are quantized and entropy coded by Embedded Block Coding with Optimized Truncations (EBCOT). Therefore, we are able to encode the input video into multiple quality layers with sequential decoding dependency. A ...

  2. Bounds and asymptotics for orthogonal polynomials for varying weights

    CERN Document Server

    Levin, Eli


    This book establishes bounds and asymptotics under almost minimal conditions on the varying weights, and applies them to universality limits and entropy integrals.  Orthogonal polynomials associated with varying weights play a key role in analyzing random matrices and other topics.  This book will be of use to a wide community of mathematicians, physicists, and statisticians dealing with techniques of potential theory, orthogonal polynomials, approximation theory, as well as random matrices. .

  3. Natural selection promotes antigenic evolvability

    NARCIS (Netherlands)

    Graves, C.J.; Ros, V.I.D.; Stevenson, B.; Sniegowski, P.D.; Brisson, D.


    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide

  4. Disgust: Evolved function and structure

    NARCIS (Netherlands)

    Tybur, J.M.; Lieberman, D.; Kurzban, R.; DeScioli, P.


    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and

  5. Regulation of bacterial gene expression by ribosome stalling and rescuing. (United States)

    Jin, Yongxin; Jin, Shouguang; Wu, Weihui


    Ribosome is responsible for protein synthesis and is able to monitor the sequence and structure of the nascent peptide. Such ability plays an important role in determining overall gene expression profile of the bacteria through ribosome stalling and rescuing. In this review, we briefly summarize our current understanding of the regulation of gene expression through ribosome stalling and rescuing in bacteria, as well as mechanisms that modulate ribosome activity. Understanding the mechanisms of how bacteria modulate ribosome activity will provide not only fundamental insights into bacterial gene regulation, but also new candidate targets for the development of novel antimicrobial agents.

  6. Evolving virtual creatures and catapults. (United States)

    Chaumont, Nicolas; Egli, Richard; Adami, Christoph


    We present a system that can evolve the morphology and the controller of virtual walking and block-throwing creatures (catapults) using a genetic algorithm. The system is based on Sims' work, implemented as a flexible platform with an off-the-shelf dynamics engine. Experiments aimed at evolving Sims-type walkers resulted in the emergence of various realistic gaits while using fairly simple objective functions. Due to the flexibility of the system, drastically different morphologies and functions evolved with only minor modifications to the system and objective function. For example, various throwing techniques evolved when selecting for catapults that propel a block as far as possible. Among the strategies and morphologies evolved, we find the drop-kick strategy, as well as the systematic invention of the principle behind the wheel, when allowing mutations to the projectile.

  7. Non-Archimedean analogues of orthogonal and symmetric operators

    Energy Technology Data Exchange (ETDEWEB)

    Albeverio, S [Mathematischer Institut, Ruhr-Universitat (Germany); Bayod, J M; Perez-Garsia, C; Khrennikov, A Yu; Cianci, R


    We study orthogonal and symmetric operators on non-Archimedean Hilbert spaces in connection with the p-adic quantization. This quantization describes measurements with finite precision. Symmetric (bounded) operators on p-adic Hilbert spaces represent physical observables. We study the spectral properties of one of the most important quantum operators, namely, the position operator (which is represented on p-adic Hilbert L{sub 2}-space with respect to the p-adic Gaussian measure). Orthogonal isometric isomorphisms of p-adic Hilbert spaces preserve the precision of measurements. We study properties of orthogonal operators. It is proved that every orthogonal operator on non-Archimedean Hilbert space is continuous. However, there are discontinuous operators with dense domain of definition that preserve the inner product. There exist non-isometric orthogonal operators. We describe some classes of orthogonal isometric operators on finite-dimensional spaces. We study some general questions in the theory of non-Archimedean Hilbert spaces (in particular, general connections between the topology, norm and inner product)

  8. Orthogonality of binary codes derived from Reed-Solomon codes (United States)

    Retter, Charles T.


    A simple method is developed for determining the orthogonality of binary codes derived from Reed-Solomon codes and other cyclic codes of length (2 exp m) - 1 over GF(2 exp m) for m bits. Depending on the spectra of the codes, it is sufficient to test a small number of single-frequency pairs for orthogonality, and a pair of bases may be tested in each case simply by summing the appropriate powers of elements of the dual bases. This simple test can be used to find self-orthogonal codes. For even values of m, the author presents a technique that can be used to choose a basis that produces a self-orthogonal, doubly-even code in certain cases, particularly when m is highly composite. If m is a power of 2, this technique can be used to find self-dual bases for GF(2 exp m). Although the primary emphasis is on testing for self orthogonality, the fundamental theorems presented apply also to the orthogonality of two different codes.

  9. Ribosome Mediated Quinary Interactions Modulate In-Cell Protein Activities. (United States)

    DeMott, Christopher M; Majumder, Subhabrata; Burz, David S; Reverdatto, Sergey; Shekhtman, Alexander


    Ribosomes are present inside bacterial cells at micromolar concentrations and occupy up to 20% of the cell volume. Under these conditions, even weak quinary interactions between ribosomes and cytosolic proteins can affect protein activity. By using in-cell and in vitro NMR spectroscopy, and biophysical techniques, we show that the enzymes, adenylate kinase and dihydrofolate reductase, and the respective coenzymes, ATP and NADPH, bind to ribosomes with micromolar affinity, and that this interaction suppresses the enzymatic activities of both enzymes. Conversely, thymidylate synthase, which works together with dihydrofolate reductase in the thymidylate synthetic pathway, is activated by ribosomes. We also show that ribosomes impede diffusion of green fluorescent protein in vitro and contribute to the decrease in diffusion in vivo. These results strongly suggest that ribosome-mediated quinary interactions contribute to the differences between in vitro and in vivo protein activities and that ribosomes play a previously under-appreciated nontranslational role in regulating cellular biochemistry.

  10. Translational control of ribosomal protein S15. (United States)

    Portier, C; Philippe, C; Dondon, L; Grunberg-Manago, M; Ebel, J P; Ehresmann, B; Ehresmann, C


    The expression of ribosomal protein S15 is shown to be translationally and negatively autocontrolled using a fusion within a reporter gene. Isolation and characterization of several deregulated mutants indicate that the regulatory site (the translational operator site) overlaps the ribosome loading site of the S15 messenger. In this region, three domains, each exhibiting a stem-loop structure, were determined using chemical and enzymatic probes. The most downstream hairpin carries the Shine-Dalgarno sequence and the initiation codon. Genetic and structural data derived from mutants constructed by site-directed mutagenesis show that the operator is a dynamic structure, two domains of which can form a pseudoknot. Binding of S15 to these two domains suggests that the pseudoknot could be stabilized by S15. A model is presented in which two alternative structures would explain the molecular basis of the S15 autocontrol.

  11. Structural snapshots of actively translating human ribosomes. (United States)

    Behrmann, Elmar; Loerke, Justus; Budkevich, Tatyana V; Yamamoto, Kaori; Schmidt, Andrea; Penczek, Pawel A; Vos, Matthijn R; Bürger, Jörg; Mielke, Thorsten; Scheerer, Patrick; Spahn, Christian M T


    Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical machines, a crucial difference is that, at the molecular dimension, thermodynamic effects dominate functional cycles, with proteins fluctuating stochastically between functional states defined by energetic minima on an energy landscape. Here, we have used cryo-electron microscopy to image ex-vivo-derived human polysomes as a source of actively translating ribosomes. Multiparticle refinement and 3D variability analysis allowed us to visualize a variety of native translation intermediates. Significantly populated states include not only elongation cycle intermediates in pre- and post-translocational states, but also eEF1A-containing decoding and termination/recycling complexes. Focusing on the post-translocational state, we extended this assessment to the single-residue level, uncovering striking details of ribosome-ligand interactions and identifying both static and functionally important dynamic elements. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Disassembly of yeast 80S ribosomes into subunits is a concerted action of ribosome-assisted folding of denatured protein. (United States)

    Chakraborty, Biprashekhar; Bhakta, Sayan; Sengupta, Jayati


    It has been shown by several groups that ribosome can assist folding of denatured protein in vitro and the process is conserved across the species. Domain V of large ribosomal rRNA which occupies the intersubunit side of the large subunit was identified as the key player responsible for chaperoning the folding process. Thus, it is conceivable that denatured protein needs to access the intersubunit space of the ribosome in order to get folded. In this study, we have investigated the mechanism of release of the protein from the eukaryotic ribosome following reactivation. We have observed significant splitting of yeast 80S ribosome when incubated with the denatured BCAII protein. Energy-free disassembly mechanism functions in low Mg(+2) ion concentration for prokaryotic ribosomes. Eukaryotic ribosomes do not show significant splitting even at low Mg(+2) ion concentration. In this respect, denatured protein-induced disassembly of eukaryotic ribosome without the involvement of any external energy source is intriguing. For prokaryotic ribosomes, it was reported that the denatured protein induces ribosome splitting into subunits in order to access domain V-rRNA. In contrast, our results suggest an alternative mechanism for eukaryotic ribosomal rRNA-mediated protein folding and subsequent separation of the subunits by which release of the activated-protein occurs. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Computation of the Likelihood in Biallelic Diffusion Models Using Orthogonal Polynomials

    Directory of Open Access Journals (Sweden)

    Claus Vogl


    Full Text Available In population genetics, parameters describing forces such as mutation, migration and drift are generally inferred from molecular data. Lately, approximate methods based on simulations and summary statistics have been widely applied for such inference, even though these methods waste information. In contrast, probabilistic methods of inference can be shown to be optimal, if their assumptions are met. In genomic regions where recombination rates are high relative to mutation rates, polymorphic nucleotide sites can be assumed to evolve independently from each other. The distribution of allele frequencies at a large number of such sites has been called “allele-frequency spectrum” or “site-frequency spectrum” (SFS. Conditional on the allelic proportions, the likelihoods of such data can be modeled as binomial. A simple model representing the evolution of allelic proportions is the biallelic mutation-drift or mutation-directional selection-drift diffusion model. With series of orthogonal polynomials, specifically Jacobi and Gegenbauer polynomials, or the related spheroidal wave function, the diffusion equations can be solved efficiently. In the neutral case, the product of the binomial likelihoods with the sum of such polynomials leads to finite series of polynomials, i.e., relatively simple equations, from which the exact likelihoods can be calculated. In this article, the use of orthogonal polynomials for inferring population genetic parameters is investigated.

  14. When did oxygenic photosynthesis evolve?

    National Research Council Canada - National Science Library

    Roger Buick


    ...2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event...

  15. Marshal: Maintaining Evolving Models Project (United States)

    National Aeronautics and Space Administration — SIFT proposes to design and develop the Marshal system, a mixed-initiative tool for maintaining task models over the course of evolving missions. Marshal-enabled...

  16. Quantifying ribosome dynamics in Escherichia coli using fluorescence. (United States)

    Failmezger, Jurek; Ludwig, Julian; Nieß, Alexander; Siemann-Herzberg, Martin


    Ribosomes are a crucial component of the physiological state of a cell. Therefore, we aimed to monitor ribosome dynamics using a fast and easy fluorescence readout. Using fluorescent-labeled ribosomal proteins, the dynamics of ribosomes during batch cultivation and during nutritional shift conditions was investigated. The fluorescence readout was compared to the cellular rRNA content determined by capillary gel electrophoresis with laser-induced fluorescence detection during exponentially accelerating and decelerating growth. We found a linear correlation between the observed fluorescence and the extracted rRNA content throughout cultivation, demonstrating the applicability of this method. Moreover, the results show that ribosome dynamics, as a result of slowing growth, are accompanied by the passive effect of dilution of preexisting ribosomes, de novo ribosome synthesis and ribosome degradation. In light of the challenging task of deciphering ribosome regulatory mechanisms, our approach of using fluorescence to follow ribosome dynamics will allow more comprehensive studies of biological systems. © FEMS 2017. All rights reserved. For permissions, please e-mail:

  17. Natural selection promotes antigenic evolvability. (United States)

    Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin


    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

  18. Natural selection promotes antigenic evolvability.

    Directory of Open Access Journals (Sweden)

    Christopher J Graves

    Full Text Available The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish

  19. The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. (United States)

    Barkan, Alice; Klipcan, Larik; Ostersetzer, Oren; Kawamura, Tetsuya; Asakura, Yukari; Watkins, Kenneth P


    The CRS1-YhbY domain (also called the CRM domain) is represented as a stand-alone protein in Archaea and Bacteria, and in a family of single- and multidomain proteins in plants. The function of this domain is unknown, but structural data and the presence of the domain in several proteins known to interact with RNA have led to the proposal that it binds RNA. Here we describe a phylogenetic analysis of the domain, its incorporation into diverse proteins in plants, and biochemical properties of a prokaryotic and eukaryotic representative of the domain family. We show that a bacterial member of the family, Escherichia coli YhbY, is associated with pre-50S ribosomal subunits, suggesting that YhbY functions in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. We show further that an isolated maize CRM domain has RNA binding activity in vitro, and that a small motif shared with KH RNA binding domains, a conserved "GxxG" loop, contributes to its RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes.

  20. ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. (United States)

    Sundaramoorthy, Elayanambi; Leonard, Marilyn; Mak, Raymond; Liao, Jeffrey; Fulzele, Amitkumar; Bennett, Eric J


    Ribosomes that experience terminal stalls during translation are resolved by ribosome-associated quality control (QC) pathways that oversee mRNA and nascent chain destruction and recycle ribosomal subunits. The proximal factors that sense stalled ribosomes and initiate mammalian ribosome-associated QC events remain undefined. We demonstrate that the ZNF598 ubiquitin ligase and the 40S ribosomal protein RACK1 help to resolve poly(A)-induced stalled ribosomes. They accomplish this by regulating distinct and overlapping regulatory 40S ribosomal ubiquitylation events. ZNF598 primarily mediates regulatory ubiquitylation of RPS10 and RPS20, whereas RACK1 regulates RPS2, RPS3, and RPS20 ubiquitylation. Gain or loss of ZNF598 function or mutations that block RPS10 or RPS20 ubiquitylation result in defective resolution of stalled ribosomes and subsequent readthrough of poly(A)-containing stall sequences. Together, our results indicate that ZNF598, RACK1, and 40S regulatory ubiquitylation plays a pivotal role in mammalian ribosome-associated QC pathways. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. The ribosomal protein Rpl22 controls ribosome composition by directly repressing expression of its own paralog, Rpl22l1.

    Directory of Open Access Journals (Sweden)

    Monique N O'Leary

    Full Text Available Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions. In yeast, ribosomal protein genes are generally duplicated and evidence has emerged that paralogs might have specific roles. Unlike yeast, most mammalian ribosomal proteins are thought to be encoded by a single gene copy, raising the possibility that heterogenous populations of ribosomes are unique to yeast. Here, we examine the roles of the mammalian Rpl22, finding that Rpl22(-/- mice have only subtle phenotypes with no significant translation defects. We find that in the Rpl22(-/- mouse there is a compensatory increase in Rpl22-like1 (Rpl22l1 expression and incorporation into ribosomes. Consistent with the hypothesis that either ribosomal protein can support translation, knockdown of Rpl22l1 impairs growth of cells lacking Rpl22. Mechanistically, Rpl22 regulates Rpl22l1 directly by binding to an internal hairpin structure and repressing its expression. We propose that ribosome specificity may exist in mammals, providing evidence that one ribosomal protein can influence composition of the ribosome by regulating its own paralog.

  2. Orthogonal test and experimental study on fire floating pump (United States)

    Liu, J. R.; Zheng, J. F.; Fu, D. P.; Wang, P.


    In order to develop high efficiency fire floating pump, 250YYB-250 fire floating pump was taken as an example. The orthogonal experiment of L9 (34), which contains factors with three levels of blade numbers of impeller, outlet angle, impeller fold-angle, was performed to design nine types of impellers. Numerical simulation of whole flow field based on Fluent was adopted to perform an orthogonal test, the order of geometric parameters affects the performance of fire floating pump with complex impeller. The best design scheme for pump model was acquired. Meanwhile, the optimized design scheme was determined, and corresponding test was carried out. It demonstrated that the efficiency of the final optimal design model pump at rated flow point is of 85%. The efficiency is higher than the national standards, which verified the feasibility of the method of orthogonal design in pump design.

  3. Orthogonal chemical functionalization of patterned gold on silica surfaces

    Directory of Open Access Journals (Sweden)

    Francisco Palazon


    Full Text Available Single-step orthogonal chemical functionalization procedures have been developed with patterned gold on silica surfaces. Different combinations of a silane and a thiol were simultaneously deposited on a gold/silica heterogeneous substrate. The orthogonality of the functionalization (i.e., selective grafting of the thiol on the gold areas and the silane on the silica was demonstrated by X-ray photoelectron spectroscopy (XPS as well as time-of-flight secondary ion mass spectrometry (ToF–SIMS mapping. The orthogonal functionalization was used to immobilize proteins onto gold nanostructures on a silica substrate, as demonstrated by atomic force microscopy (AFM. These results are especially promising in the development of future biosensors where the selective anchoring of target molecules onto nanostructured transducers (e.g., nanoplasmonic biosensors is a major challenge.

  4. Orthogonal functions, discrete variable representation, and generalized gauss quadratures

    DEFF Research Database (Denmark)

    Schneider, B. I.; Nygaard, Nicolai


    , the distinction between spectral and grid approaches becomes blurred. In fact, the two approaches can be related by a similarity transformation. By the exploitation of this idea, calculations can be considerably simplified by removing the need to compute difficult matrix elements of the Hamiltonian...... in the original representation. This has been exploited in bound-state, scattering, and time-dependent problems using the so-called, discrete variable representation (DVR). At the core of this approach is the mathematical three-term recursion relationship satisfied by the classical orthogonal functions....... This three-term recursion can be used to generate the orthogonal functions as well as to generate the points and weights of Gauss quadratures on the basis of these functions. For the classical orthogonal functions, the terms in the three-term recursion are known analytically. For more general weight...

  5. Recurrence Relations for Orthogonal Polynomials on Triangular Domains

    Directory of Open Access Journals (Sweden)

    Abedallah Rababah


    Full Text Available In Farouki et al, 2003, Legendre-weighted orthogonal polynomials P n , r ( u , v , w , r = 0 , 1 , … , n , n ≥ 0 on the triangular domain T = { ( u , v , w : u , v , w ≥ 0 , u + v + w = 1 } are constructed, where u , v , w are the barycentric coordinates. Unfortunately, evaluating the explicit formulas requires many operations and is not very practical from an algorithmic point of view. Hence, there is a need for a more efficient alternative. A very convenient method for computing orthogonal polynomials is based on recurrence relations. Such recurrence relations are described in this paper for the triangular orthogonal polynomials, providing a simple and fast algorithm for their evaluation.

  6. Active yeast ribosome preparation using monolithic anion exchange chromatography. (United States)

    Munoz, Antonio M; Yourik, Paul; Rajagopal, Vaishnavi; Nanda, Jagpreet S; Lorsch, Jon R; Walker, Sarah E


    In vitro studies of translation provide critical mechanistic details, yet purification of large amounts of highly active eukaryotic ribosomes remains a challenge for biochemists and structural biologists. Here, we present an optimized method for preparation of highly active yeast ribosomes that could easily be adapted for purification of ribosomes from other species. The use of a nitrogen mill for cell lysis coupled with chromatographic purification of the ribosomes results in 10-fold-increased yield and less variability compared with the traditional approach, which relies on sedimentation through sucrose cushions. We demonstrate that these ribosomes are equivalent to those made using the traditional method in a host of in vitro assays, and that utilization of this new method will consistently produce high yields of active yeast ribosomes.

  7. Chemical modulators of ribosome biogenesis as biological probes. (United States)

    Stokes, Jonathan M; Brown, Eric D


    Small-molecule inhibitors of protein biosynthesis have been instrumental in the dissection of the complexities of ribosome structure and function. Ribosome biogenesis, on the other hand, is a complex and largely enigmatic process for which there is a paucity of chemical probes. Indeed, ribosome biogenesis has been studied almost exclusively using genetic and biochemical approaches without the benefit of small-molecule inhibitors of this process. Here, we provide a perspective on the promise of chemical inhibitors of ribosome assembly for future research. We explore key obstacles that complicate the interpretation of studies aimed at perturbing ribosome biogenesis in vivo using genetic methods, and we argue that chemical inhibitors are especially powerful because they can be used to induce perturbations in a manner that obviates these difficulties. Thus, in combination with leading-edge biochemical and structural methods, chemical probes offer unique advantages toward elucidating the molecular events that define the assembly of ribosomes.

  8. The architecture of mammalian ribosomal protein promoters

    Directory of Open Access Journals (Sweden)

    Perry Robert P


    Full Text Available Abstract Background Mammalian ribosomes contain 79 different proteins encoded by widely scattered single copy genes. Coordinate expression of these genes at transcriptional and post-transcriptional levels is required to ensure a roughly equimolar accumulation of ribosomal proteins. To date, detailed studies of only a very few ribosomal protein (rp promoters have been made. To elucidate the general features of rp promoter architecture, I made a detailed sequence comparison of the promoter regions of the entire set of orthologous human and mouse rp genes. Results A striking evolutionarily conserved feature of most rp genes is the separation by an intron of the sequences involved in transcriptional and translational regulation from the sequences with protein encoding function. Another conserved feature is the polypyrimidine initiator, which conforms to the consensus (Y2C+1TY(T2(Y3. At least 60 % of the rp promoters contain a largely conserved TATA box or A/T-rich motif, which should theoretically have TBP-binding capability. A remarkably high proportion of the promoters contain conserved binding sites for transcription factors that were previously implicated in rp gene expression, namely upstream GABP and Sp1 sites and downstream YY1 sites. Over 80 % of human and mouse rp genes contain a transposable element residue within 900 bp of 5' flanking sequence; very little sequence identity between human and mouse orthologues was evident more than 200 bp upstream of the transcriptional start point. Conclusions This analysis has provided some valuable insights into the general architecture of mammalian rp promoters and has identified parameters that might coordinately regulate the transcriptional activity of certain subsets of rp genes.

  9. Placeholder factors in ribosome biogenesis: please, pave my way

    Directory of Open Access Journals (Sweden)

    Francisco J. Espinar-Marchena


    Full Text Available The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and some ribosomal proteins to form pre-ribosomal particles. These factors include snoRNPs, nucleases, ATPases, GTPases, RNA helicases, and a vast list of proteins with no predicted enzymatic activity. Their coordinate activity orchestrates in a spatiotemporal manner the modification and processing of precursor rRNAs, the rearrangement reactions required for the formation of productive RNA folding intermediates, the ordered assembly of the ribosomal proteins, and the export of pre-ribosomal particles to the cytoplasm; thus, providing speed, directionality and accuracy to the overall process of formation of translation-competent ribosomes. Here, we review a particular class of trans-acting factors known as “placeholders”. Placeholder factors temporarily bind selected ribosomal sites until these have achieved a structural context that is appropriate for exchanging the placeholder with another site-specific binding factor. By this strategy, placeholders sterically prevent premature recruitment of subsequently binding factors, premature formation of structures, avoid possible folding traps, and act as molecular clocks that supervise the correct progression of pre-ribosomal particles into functional ribosomal subunits. We summarize the current understanding of those factors that delay the assembly of distinct ribosomal proteins or subsequently bind key sites in pre-ribosomal particles. We also discuss recurrent examples of RNA-protein and protein-protein mimicry between rRNAs and/or factors, which have clear functional implications for the ribosome biogenesis pathway.

  10. A Cluster-Based Orthogonal Multi-Objective Genetic Algorithm (United States)

    Zhu, Jiankai; Dai, Guangming; Mo, Li

    Multi-objective genetic algorithm is proved to be suitable for solving multi-objective optimization problems. However, it is usually very hard to balance the convergence and diversity of a multi-objective genetic algorithm. This paper introduces a new algorithm, with both good convergence and diversity based on clustering method and multi-parent crossover operator. Meanwhile, an initial population is generated by orthogonal design to enhance the search effort of the algorithm. The experimental results on a number of test problems indicate the good performance of the Cluster-Based Orthogonal Multi-Objective Genetic Algorithm.

  11. Orthogonal Expansions for VIX Options Under Affine Jump Diffusions

    DEFF Research Database (Denmark)

    Barletta, Andrea; Nicolato, Elisa


    In this work we derive new closed–form pricing formulas for VIX options in the jump-diffusion SVJJ model proposed by Duffie et al. (2000). Our approach is based on the classic methodology of approximating a density function with an orthogonal expansion of polynomials weighted by a kernel. Orthogo......In this work we derive new closed–form pricing formulas for VIX options in the jump-diffusion SVJJ model proposed by Duffie et al. (2000). Our approach is based on the classic methodology of approximating a density function with an orthogonal expansion of polynomials weighted by a kernel...

  12. Ribosomal RNA gene functioning in avian oogenesis. (United States)

    Koshel, Elena; Galkina, Svetlana; Saifitdinova, Alsu; Dyomin, Alexandr; Deryusheva, Svetlana; Gaginskaya, Elena


    Despite long-term exploration into ribosomal RNA gene functioning during the oogenesis of various organisms, many intriguing problems remain unsolved. In this review, we describe nucleolus organizer region (NOR) activity in avian oocytes. Whereas oocytes from an adult avian ovary never reveal the formation of the nucleolus in the germinal vesicle (GV), an ovary from juvenile birds possesses both nucleolus-containing and non-nucleolus-containing oocytes. The evolutionary diversity of oocyte NOR functioning and the potential non-rRNA-related functions of the nucleolus in oocytes are also discussed.

  13. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori


    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  14. Ribosome Footprint Profiling of Translation throughout the Genome (United States)

    Ingolia, Nicholas T.


    Ribosome profiling has emerged as a technique for measuring translation comprehensively and quantitatively by deep sequencing of ribosome-protected mRNA fragments. By identifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into the composition and regulation of the expressed proteome, including delineating potentially functional micropeptides, revealing pervasive translation on cytosolic RNAs, and identifying differences in elongation rates driven by codon usage or other factors. This Primer looks at important experimental and analytical concerns for executing ribosome profiling experiments and surveys recent examples where the approach was developed to explore protein biogenesis and homeostasis. PMID:27015305

  15. Dynamic Behavior of Trigger Factor on the Ribosome. (United States)

    Deeng, J; Chan, K Y; van der Sluis, E O; Berninghausen, O; Han, W; Gumbart, J; Schulten, K; Beatrix, B; Beckmann, R


    Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Complete kinetic mechanism for recycling of the bacterial ribosome. (United States)

    Borg, Anneli; Pavlov, Michael; Ehrenberg, Måns


    How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec(-1), is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec(-1), are discussed in the perspective of rapidly growing bacterial cells. © 2015 Borg et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  17. Ribosome hibernation factor promotes Staphylococcal survival and differentially represses translation. (United States)

    Basu, Arnab; Yap, Mee-Ngan F


    In opportunistic Gram-positive Staphylococcus aureus, a small protein called hibernation-promoting factor (HPFSa) is sufficient to dimerize 2.5-MDa 70S ribosomes into a translationally inactive 100S complex. Although the 100S dimer is observed in only the stationary phase in Gram-negative gammaproteobacteria, it is ubiquitous throughout all growth phases in S. aureus The biological significance of the 100S ribosome is poorly understood. Here, we reveal an important role of HPFSa in preserving ribosome integrity and poising cells for translational restart, a process that has significant clinical implications for relapsed staphylococcal infections. We found that the hpf null strain is severely impaired in long-term viability concomitant with a dramatic loss of intact ribosomes. Genome-wide ribosome profiling shows that eliminating HPFSa drastically increased ribosome occupancy at the 5' end of specific mRNAs under nutrient-limited conditions, suggesting that HPFSa may suppress translation initiation. The protective function of HPFSa on ribosomes resides at the N-terminal conserved basic residues and the extended C-terminal segment, which are critical for dimerization and ribosome binding, respectively. These data provide significant insight into the functional consequences of 100S ribosome loss for protein synthesis and stress adaptation. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. (United States)

    Reid, David W; Nicchitta, Christopher V


    In eukaryotic cells, the spatial regulation of protein expression is frequently conferred through the coupling of mRNA localization and the local control of translation. mRNA localization to the endoplasmic reticulum (ER) is a prominent example of such regulation and serves a ubiquitous role in segregating the synthesis of secretory and integral membrane proteins to the ER. Recent genomic and biochemical studies have now expanded this view to suggest a more substantial role for the ER cellular protein synthesis. We have utilized cell fractionation and ribosome profiling to obtain a genomic survey of the subcellular organization of mRNA translation and report that ribosomal loading of mRNAs, a proxy for mRNA translation, is biased to the ER. Notably, ER-associated mRNAs encoding both cytosolic and topogenic signal-encoding proteins display similar ribosome loading densities, suggesting that ER-associated ribosomes serve a global role in mRNA translation. We propose that the partitioning of mRNAs and their translation between the cytosol and ER compartments may represent a novel mechanism for the post-transcriptional regulation of gene expression.

  19. Transition state analogues rescue ribosomes from saporin-L1 ribosome inactivating protein. (United States)

    Sturm, Matthew B; Tyler, Peter C; Evans, Gary B; Schramm, Vern L


    Ribosome inactivating proteins (RIPs) catalyze the hydrolytic depurination of one or more adenosine residues from eukaryotic ribosomes. Depurination of the ribosomal sarcin-ricin tetraloop (GAGA) causes inhibition of protein synthesis and cellular death. We characterized the catalytic properties of saporin-L1 from Saponaria officinalis (soapwort) leaves, and it demonstrated robust activity against defined nucleic acid substrates and mammalian ribosomes. Transition state analogue mimics of small oligonucleotide substrates of saporin-L1 are powerful, slow-onset inhibitors when adenosine is replaced with the transition state mimic 9-deazaadenine-9-methylene-N-hydroxypyrrolidine (DADMeA). Linear, cyclic, and stem-loop oligonucleotide inhibitors containing DADMeA and based on the GAGA sarcin-ricin tetraloop gave slow-onset tight-binding inhibition constants (K(i)*) of 2.3-8.7 nM under physiological conditions and bind up to 40000-fold tighter than RNA substrates. Saporin-L1 inhibition of rabbit reticulocyte translation was protected by these inhibitors. Transition state analogues of saporin-L1 have potential in cancer therapy that employs saporin-L1-linked immunotoxins.

  20. A Molecular Titration System Coordinates Ribosomal Protein Gene Transcription with Ribosomal RNA Synthesis. (United States)

    Albert, Benjamin; Knight, Britta; Merwin, Jason; Martin, Victoria; Ottoz, Diana; Gloor, Yvonne; Bruzzone, Maria Jessica; Rudner, Adam; Shore, David


    Cell growth potential is determined by the rate of ribosome biogenesis, a complex process that requires massive and coordinated transcriptional output. In the yeast Saccharomyces cerevisiae, ribosome biogenesis is highly regulated at the transcriptional level. Although evidence for a system that coordinates ribosomal RNA (rRNA) and ribosomal protein gene (RPG) transcription has been described, the molecular mechanisms remain poorly understood. Here we show that an interaction between the RPG transcriptional activator Ifh1 and the rRNA processing factor Utp22 serves to coordinate RPG transcription with that of rRNA. We demonstrate that Ifh1 is rapidly released from RPG promoters by a Utp22-independent mechanism following growth inhibition, but that its long-term dissociation requires Utp22. We present evidence that RNA polymerase I activity inhibits the ability of Utp22 to titrate Ifh1 from RPG promoters and propose that a dynamic Ifh1-Utp22 interaction fine-tunes RPG expression to coordinate RPG and rRNA transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Phosphorylation of acidic ribosomal proteins from rabbit reticulocytes by a ribosome-associated casein kinase

    DEFF Research Database (Denmark)

    Issinger, O G


    Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate polyacryl...

  2. In Profile: Models of Ribosome Biogenesis Defects and Regulation of Protein Synthesis

    NARCIS (Netherlands)

    Essers, P.B.M.


    Ribosomes are the mediators of protein synthesis in the cell and therefore crucial to proper cell function. In addition, ribosomes are highly abundant, with ribosomal RNA making up 80% of the RNA in the cell. A large amount of resources go into maintaining this pool of ribosomes, so ribosome

  3. A conserved domain important for association of eukaryotic J-protein co-chaperones Jjj1 and Zuo1 with the ribosome. (United States)

    Kaschner, Lindsey A; Sharma, Ruchika; Shrestha, Om Kumar; Meyer, Alison E; Craig, Elizabeth A


    J-proteins, obligate co-chaperones, provide specialization for Hsp70 function in a variety of cellular processes. Two of the 13 J-proteins of the yeast cytosol/nucleus, Zuo1 and Jjj1, are associated with 60S ribosomal subunits. Abundant Zuo1 facilitates folding of nascent polypeptides; Jjj1, of much lower abundance, functions in ribosome biogenesis. However, overexpression of Jjj1 substantially rescues growth defects of cells lacking Zuo1. We analyzed a region held in common by Zuo1 and Jjj1, outside the signature J-domain found in all J-proteins. This shared "zuotin homology domain" (ZHD) is important for ribosome association of both proteins. An N-terminal segment of Jjj1, containing the J-domain and ZHD, is ribosome-associated and, like full-length Jjj1, is competent to rescue both the cold- and cation-sensitivity of ∆zuo1. However, this fragment, when expressed at normal levels, cannot rescue the cytosolic ribosome biogenesis defect of ∆jjj1. Our results are consistent with a model in which the primary functions of Zuo1 and Jjj1 occur in the cytosol. In addition, our data suggest that Zuo1 and Jjj1 bind overlapping sites on ribosomes due to an interaction via their common ZHDs, but Jjj1 binds primarily to pre-60S particles and Zuo1 to mature subunits. We hypothesize that ZUO1 and JJJ1, which are conserved throughout eukaryotes, arose from an ancient duplication of a progenitor J-protein gene that encoded the ZHD ribosome-binding region; subsequently, specialized roles and additional ribosome interaction sites evolved. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Ribosome Flow Model on a Ring. (United States)

    Raveh, Alon; Zarai, Yoram; Margaliot, Michael; Tuller, Tamir


    The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered lattice of sites, but only if the next site is empty. ASEP has been used to model and analyze numerous multiagent systems with local interactions including the flow of ribosomes along the mRNA strand. In ASEP with periodic boundary conditions a particle that hops from the last site returns to the first one. The mean field approximation of this model is referred to as the ribosome flow model on a ring (RFMR). The RFMR may be used to model both synthetic and endogenous gene expression regimes. We analyze the RFMR using the theory of monotone dynamical systems. We show that it admits a continuum of equilibrium points and that every trajectory converges to an equilibrium point. Furthermore, we show that it entrains to periodic transition rates between the sites. We describe the implications of the analysis results to understanding and engineering cyclic mRNA translation in-vitro and in-vivo.

  5. Defining the bacteroides ribosomal binding site. (United States)

    Wegmann, Udo; Horn, Nikki; Carding, Simon R


    The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus Bacteroides are among the most abundant bacterial species in the human colon. Bacteroidetes diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in Bacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of pepI from Lactobacillus delbrueckii subsp. lactis as a novel reporter gene for Bacteroides. Furthermore, we report the identification of the 3' end of the 16S rRNA of Bacteroides ovatus and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5' untranslated region of other Bacteroidales ribosomal protein genes, we conclude that our findings are relevant to all members of this order.

  6. Sparsely-Packetized Predictive Control by Orthogonal Matching Pursuit

    DEFF Research Database (Denmark)

    Nagahara, Masaaki; Quevedo, Daniel; Østergaard, Jan


    We study packetized predictive control, known to be robust against packet dropouts in networked systems. To obtain sparse packets for rate-limited networks, we design control packets via an ℓ0 optimization, which can be eectively solved by orthogonal matching pursuit. Our formulation ensures...

  7. On orthogonal systems in Hilbert C*-modules


    Landi, Giovanni; Pavlov, Alexander


    Analogues for Hilbert C*-modules of classical results of Fourier series theory in Hilbert spaces are considered. Relations between different properties of orthogonal and orthonormal systems for Hilbert C*-modules are studied with special attention paid on the differences with the well-known Hilbert space situation.

  8. Batch-Orthogonal Locality-Sensitive Hashing for Angular Similarity. (United States)

    Ji, Jianqiu; Yan, Shuicheng; Li, Jianmin; Gao, Guangyu; Tian, Qi; Zhang, Bo


    Sign-random-projection locality-sensitive hashing (SRP-LSH) is a widely used hashing method, which provides an unbiased estimate of pairwise angular similarity, yet may suffer from its large estimation variance. We propose in this work batch-orthogonal locality-sensitive hashing (BOLSH), as a significant improvement of SRP-LSH. Instead of independent random projections, BOLSH makes use of batch-orthogonalized random projections, i.e, we divide random projection vectors into several batches and orthogonalize the vectors in each batch respectively. These batch-orthogonalized random projections partition the data space into regular regions, and thus provide a more accurate estimator. We prove theoretically that BOLSH still provides an unbiased estimate of pairwise angular similarity, with a smaller variance for any angle in (0, π), compared with SRP-LSH. Furthermore, we give a lower bound on the reduction of variance. The extensive experiments on real data well validate that with the same length of binary code, BOLSH may achieve significant mean squared error reduction in estimating pairwise angular similarity. Moreover, BOLSH shows the superiority in extensive approximate nearest neighbor (ANN) retrieval experiments.

  9. Secrecy Capacity of a Class of Orthogonal Relay Eavesdropper Channels

    Directory of Open Access Journals (Sweden)

    Vaneet Aggarwal


    Full Text Available The secrecy capacity of relay channels with orthogonal components is studied in the presence of an additional passive eavesdropper node. The relay and destination receive signals from the source on two orthogonal channels such that the destination also receives transmissions from the relay on its channel. The eavesdropper can overhear either one or both of the orthogonal channels. Inner and outer bounds on the secrecy capacity are developed for both the discrete memoryless and the Gaussian channel models. For the discrete memoryless case, the secrecy capacity is shown to be achieved by a partial decode-and-forward (PDF scheme when the eavesdropper can overhear only one of the two orthogonal channels. Two new outer bounds are presented for the Gaussian model using recent capacity results for a Gaussian multiantenna point-to-point channel with a multiantenna eavesdropper. The outer bounds are shown to be tight for two subclasses of channels. The first subclass is one in which the source and relay are clustered, and the eavesdropper receives signals only on the channel from the source and the relay to the destination, for which the PDF strategy is optimal. The second is a subclass in which the source does not transmit to the relay, for which a noise-forwarding strategy is optimal.

  10. Cardinality-dependent Variability in Orthogonal Variability Models

    DEFF Research Database (Denmark)

    Mærsk-Møller, Hans Martin; Jørgensen, Bo Nørregaard


    During our work on developing and running a software product line for eco-sustainable greenhouse-production software tools, which currently have three products members we have identified a need for extending the notation of the Orthogonal Variability Model (OVM) to support what we refer...

  11. Application of Orthogonal Design to Optimize Extraction of ...

    African Journals Online (AJOL)

    Purpose: To optimize the extraction technology of polysaccharides from Cynomorium songaricum Rupr by ultrasonic-assisted extraction (UAE). Methods: Four parameters including ultrasonic power, ratio of raw material to water, extraction temperature, and extraction time were optimized by orthogonal design. The effects of ...

  12. An Orthogonal Residual Procedure for Nonlinear Finite Element Equations

    DEFF Research Database (Denmark)

    Krenk, S.

    A general and robust solution procedure for nonlinear finite element equations with limit points is developed. At each equilibrium iteration the magnitude of the load is adjusted such that the residual force is orthogonal to the current displacement increment from the last equilibrium state...

  13. Application of Orthogonal Design to Optimize Extraction of ...

    African Journals Online (AJOL)

    polysaccharides have been reported, including solvent extraction [11], biological enzymatic method [12] and ultrasonic extraction [13,14]. The aim of this study was to apply ultrasonic- assisted extraction (UAE) to isolate polysaccharides from C. songaricum, and to optimize the extraction parameters using orthogonal design ...

  14. Orthogonal designs Hadamard matrices, quadratic forms and algebras

    CERN Document Server

    Seberry, Jennifer


    Orthogonal designs have proved fundamental to constructing code division multiple antenna systems for more efficient mobile communications. Starting with basic theory, this book develops the algebra and combinatorics to create new communications modes. Intended primarily for researchers, it is also useful for graduate students wanting to understand some of the current communications coding theories.

  15. Orthogonal frequency division multiplexing with diversity for future wireless systems

    CERN Document Server

    Le, Khoa N


    The book examines several aspects of Orthogonal Frequency Division Multiplexing (OFDM) employing linear diversity techniques such as inter-carrier interference, bit error rate, peak to average power and inter-block interference. It should be a useful reference for readers interested in modern wireless communication systems.

  16. Orthogonal Projection in Teaching Regression and Financial Mathematics (United States)

    Kachapova, Farida; Kachapov, Ilias


    Two improvements in teaching linear regression are suggested. The first is to include the population regression model at the beginning of the topic. The second is to use a geometric approach: to interpret the regression estimate as an orthogonal projection and the estimation error as the distance (which is minimized by the projection). Linear…

  17. A Temporal Extension to Traditional Empirical Orthogonal Function Analysis

    DEFF Research Database (Denmark)

    Nielsen, Allan Aasbjerg; Hilger, Klaus Baggesen; Andersen, Ole Baltazar


    This paper describes the application of temporal maximum autocorrelation factor analysis to global monthly mean values of 1996-1997 sea surface temperature (SST) and sea surface height (SSH) data. This type of analysis can be considered as an extension of traditional empirical orthogonal function...

  18. modelling of responses from orthogonal metal cutting of mild steel

    African Journals Online (AJOL)


    The purpose of this research was to develop models for the prediction of responses from orthogonal metal cutting process that are responsible for the machinability ratings of this technological system. Mild steel work-piece material that is representative sample for various industrial applications was machined. The various ...

  19. Adaptive integrand decomposition in parallel and orthogonal space

    Energy Technology Data Exchange (ETDEWEB)

    Mastrolia, Pierpaolo [Dipartimento di Fisica ed Astronomia, Università di Padova,Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova,Via Marzolo 8, 35131 Padova (Italy); Peraro, Tiziano [Higgs Centre for Theoretical Physics, School of Physics and Astronomy,The University of Edinburgh,James Clerk Maxwell Building,Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland (United Kingdom); Primo, Amedeo [Dipartimento di Fisica ed Astronomia, Università di Padova,Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova,Via Marzolo 8, 35131 Padova (Italy)


    We present the integrand decomposition of multiloop scattering amplitudes in parallel and orthogonal space-time dimensions, d=d{sub ∥}+d{sub ⊥}, being d{sub ∥} the dimension of the parallel space spanned by the legs of the diagrams. When the number n of external legs is n≤4, the corresponding representation of multiloop integrals exposes a subset of integration variables which can be easily integrated away by means of Gegenbauer polynomials orthogonality condition. By decomposing the integration momenta along parallel and orthogonal directions, the polynomial division algorithm is drastically simplified. Moreover, the orthogonality conditions of Gegenbauer polynomials can be suitably applied to integrate the decomposed integrand, yielding the systematic annihilation of spurious terms. Consequently, multiloop amplitudes are expressed in terms of integrals corresponding to irreducible scalar products of loop momenta and external ones. We revisit the one-loop decomposition, which turns out to be controlled by the maximum-cut theorem in different dimensions, and we discuss the integrand reduction of two-loop planar and non-planar integrals up to n=8 legs, for arbitrary external and internal kinematics. The proposed algorithm extends to all orders in perturbation theory.

  20. Constructing General Orthogonal Fractional Factorial Split-Plot Designs

    NARCIS (Netherlands)

    Sartono, B.; Goos, P.; Schoen, E.


    While the orthogonal design of split-plot fractional factorial experiments has received much attention already, there are still major voids in the literature. First, designs with one or more factors acting at more than two levels have not yet been considered. Second, published work on nonregular

  1. Velocity field calculation for non-orthogonal numerical grids

    Energy Technology Data Exchange (ETDEWEB)

    Flach, G. P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)


    Computational grids containing cell faces that do not align with an orthogonal (e.g. Cartesian, cylindrical) coordinate system are routinely encountered in porous-medium numerical simulations. Such grids are referred to in this study as non-orthogonal grids because some cell faces are not orthogonal to a coordinate system plane (e.g. xy, yz or xz plane in Cartesian coordinates). Non-orthogonal grids are routinely encountered at the Savannah River Site in porous-medium flow simulations for Performance Assessments and groundwater flow modeling. Examples include grid lines that conform to the sloping roof of a waste tank or disposal unit in a 2D Performance Assessment simulation, and grid surfaces that conform to undulating stratigraphic surfaces in a 3D groundwater flow model. Particle tracking is routinely performed after a porous-medium numerical flow simulation to better understand the dynamics of the flow field and/or as an approximate indication of the trajectory and timing of advective solute transport. Particle tracks are computed by integrating the velocity field from cell to cell starting from designated seed (starting) positions. An accurate velocity field is required to attain accurate particle tracks. However, many numerical simulation codes report only the volumetric flowrate (e.g. PORFLOW) and/or flux (flowrate divided by area) crossing cell faces. For an orthogonal grid, the normal flux at a cell face is a component of the Darcy velocity vector in the coordinate system, and the pore velocity for particle tracking is attained by dividing by water content. For a non-orthogonal grid, the flux normal to a cell face that lies outside a coordinate plane is not a true component of velocity with respect to the coordinate system. Nonetheless, normal fluxes are often taken as Darcy velocity components, either naively or with accepted approximation. To enable accurate particle tracking or otherwise present an accurate depiction of the velocity field for a non-orthogonal

  2. Fast Gravitational Field Model Using Adaptive Orthogonal Finite Element Approximation (United States)

    Younes, A.; Macomber, B.; Woollands, R.; Probe, A.; Bai, X.; Junkins, J.


    Recent research has addressed the issue that high degree and order gravity expansions involve tens of thousands of terms in a theoretically infinite order spherical harmonic expansion (some gravity models extend to degree and order 200 with over 30,000 terms) which in principle must be computed at every integration step to obtain the acceleration consistent with the gravity model. We propose to evaluate these gravity model interpolation models and use them in conjunction with the modified Picard path approximation methods. It was decided to consider analogous orthogonal approximation methods to interpolate, an FEM model, high (degree, order) gravity fields, by replacing the global spherical harmonic series by a family of locally precise orthogonal polynomial approximations for efficient computation. Our preliminary results showed that time to compute the state of the art (degree and order 200) spherical harmonic gravity is reduced by 4 to 5 orders of magnitude while maintaining > 9 digits of accuracy. Most of the gain is due to adopting the orthogonal FEM approach, but radial adaptation of the approximation degree gains an additional order of magnitude speedup. The efficient data base storage/access of the local coefficients is studied, which utilizes porting the algorithm to the NVIDIA GPU. This paper will address the accuracy and efficiency in both a C++ serial PC architecture as well as a PC/GPU architecture. The Adaptive Orthogonal Finite Element Gravity Model (AOFEGM) is expected to have broad potential for speeding the trajectory propagation algorithms; for example, used in conjunction with orthogonal Finite Element Model (FEM) gravity approximations, the Chebyshev-Picard path approximation enables truly revolutionary speedups in orbit propagation without accuracy loss.

  3. Chemical Bonding: The Orthogonal Valence-Bond View

    Directory of Open Access Journals (Sweden)

    Alexander F. Sax


    Full Text Available Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO used to construct the wave functions. The transformation of such wave functions into valence bond (VB wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected.

  4. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. (United States)

    Yoshida, Hideji; Ueta, Masami; Maki, Yasushi; Sakai, Akiko; Wada, Akira


    The canonical ribosome cycle in bacteria consists of initiation, elongation, termination, and recycling stages. After the recycling stage, initiation factor 3 (IF3) stabilizes ribosomal dissociation by binding to 30S subunits for the next round of translation. On the other hand, during the stationary growth phase, it has been elucidated that Escherichia coli ribosomes are dimerized (100S ribosome formation) by binding ribosome modulation factor (RMF) and hibernation promoting factor (HPF), leading to a hibernation stage. This indicates that 100S ribosomes are formed after these factors are scrambled for ribosomes concomitantly with transition from the log phase to the stationary phase. In this study, to elucidate the ribosomal events before 100S ribosome formation, the relationships between protein factors (RMF and HPF) involved in 100S ribosome formation and IF3 involved in initiation complex formation were examined. As a result of in vitro assays, it was found that ribosomal dissociation activity by IF3 fell, and that ribosomal dimerization activity by RMF and HPF was elevated more when using stationary-phase ribosomes than when using log-phase ribosomes. This suggests that ribosomes change into forms which are hard to bind with IF3 and easy to form 100S ribosomes by RMF and HPF concomitantly with transition from the log phase to the stationary phase.

  5. An intron in a ribosomal protein gene from Tetrahymena

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Andreasen, Per Hove; Dreisig, Hanne


    of hybrid-selected mRNA and authentic ribosomal proteins. The proteins show strong homology to ribosomal protein S12 from Escherichia coli. The coding region of the gene is interrupted by a 979-bp intron 68 bp downstream of the translation start. This is the first intron in a protein encoding gene...

  6. Close sequence identity between ribosomal DNA episomes of the ...

    Indian Academy of Sciences (India)

    Entamoeba dispar and Entamoeba histolytica are now recognized as two distinct species – the former being nonpathogenic to humans. We had earlier studied the organization of ribosomal RNA genes in E. histolytica. Here we report the analysis of ribosomal RNA genes in E. dispar. The rRNA genes of E. dispar, like their ...

  7. Association of ribosomal anti-P antibodies with different parameters ...

    African Journals Online (AJOL)

    antibodies with neuropsychiatric lupus manifestations and to find out the relationship of ribosomal anti-P antibodies with other autoimmune parameters of lupus. Ribosomal anti-P antibodies were evaluated in the serum of 41 systemic lupus erythematosus (SLE) patients as well as ANA, dsDNA, anti- Sm, anti-SSA, anti-SSB, ...

  8. Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria. (United States)

    Ferrin, Michael A; Subramaniam, Arvind R


    Ribosome stalling on mRNAs can decrease protein expression. To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for the cognate amino acid. We measured protein synthesis rates from a reporter library of over 100 variants that encoded systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites. Our measurements are quantitatively inconsistent with two widely-used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. Rather, our measurements support a model in which collision with a trailing ribosome causes abortive termination of the stalled ribosome. In our computational analysis, ribosome collisions selectively stimulate abortive termination without fine-tuning of kinetic rate parameters at ribosome stall sites. We propose that ribosome collisions serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.

  9. Translation with frameshifting of ribosome along mRNA transcript

    CERN Document Server

    Li, Jingwei


    Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been developed to determine the biochemical mechanism of translation. However, to simplify the majority of the existing models, the frameshifting of ribosome along the mRNA transcript is neglected, which actually occurs in real cells and has been extensively experimentally studied. The frameshifting of ribosome evidently influences the efficiency and speed of translation, considering that the peptide chains synthesized by shifted ribosomes will not fold into functional proteins and will degrade rapidly. In this study, a theoretical model is presented to describe the translational process based on the model for totally asymmetric simple exclusion process. In this model, the frameshifting of the ribosome along the mRNA transcript and the attachment/detachment of the ribosome to/from the ...

  10. The Complete Structure of the Mycobacterium smegmatis 70S Ribosome

    Directory of Open Access Journals (Sweden)

    Jendrik Hentschel


    Full Text Available The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.

  11. The Evolving Resource Metadata Infrastructure (United States)

    Biemesderfer, Chris

    The search and discovery mechanisms that will facilitate and simplify systematic research on the Internet depend on systematic classifications of resources, as well as on standardized access to such metadata. The principles and technologies that will make this possible are evolving in the work of the Internet Engineering Task Force and the digital library initiatives, among others. The desired outcome is a set of standards, tools, and practices that permits both cataloging and retrieval to be comprehensive and efficient.

  12. Ranking in evolving complex networks (United States)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang


    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  13. Roles of Transcriptional and Translational Control Mechanisms in Regulation of Ribosomal Protein Synthesis in Escherichia coli. (United States)

    Burgos, Hector L; O'Connor, Kevin; Sanchez-Vazquez, Patricia; Gourse, Richard L


    Bacterial ribosome biogenesis is tightly regulated to match nutritional conditions and to prevent formation of defective ribosomal particles. In Escherichia coli, most ribosomal protein (r-protein) synthesis is coordinated with rRNA synthesis by a translational feedback mechanism: when r-proteins exceed rRNAs, specific r-proteins bind to their own mRNAs and inhibit expression of the operon. It was recently discovered that the second messenger nucleotide guanosine tetra and pentaphosphate (ppGpp), which directly regulates rRNA promoters, is also capable of regulating many r-protein promoters. To examine the relative contributions of the translational and transcriptional control mechanisms to the regulation of r-protein synthesis, we devised a reporter system that enabled us to genetically separate the cis-acting sequences responsible for the two mechanisms and to quantify their relative contributions to regulation under the same conditions. We show that the synthesis of r-proteins from the S20 and S10 operons is regulated by ppGpp following shifts in nutritional conditions, but most of the effect of ppGpp required the 5' region of the r-protein mRNA containing the target site for translational feedback regulation and not the promoter. These results suggest that most regulation of the S20 and S10 operons by ppGpp following nutritional shifts is indirect and occurs in response to changes in rRNA synthesis. In contrast, we found that the promoters for the S20 operon were regulated during outgrowth, likely in response to increasing nucleoside triphosphate (NTP) levels. Thus, r-protein synthesis is dynamic, with different mechanisms acting at different times.IMPORTANCE Bacterial cells have evolved complex and seemingly redundant strategies to regulate many high-energy-consuming processes. In E. coli, synthesis of ribosomal components is tightly regulated with respect to nutritional conditions by mechanisms that act at both the transcription and translation steps. In this

  14. Ribosome evolution: Emergence of peptide synthesis machinery

    Indian Academy of Sciences (India)

    Combining the present data with recent experimental data, we can infer that the peptidyl transferase center (PTC) evolved from a primitive system in the RNA world ... Department of Biological Science and Technology, 2641 Yamazaki, Noda, Chiba 278-8510( Japan; Research Institute for Science and Technology, Tokyo ...

  15. Tumor classification based on orthogonal linear discriminant analysis. (United States)

    Wang, Huiya; Zhang, Shanwen


    Gene expression profiles have great potential for accurate tumor diagnosis. It is expected to enable us to diagnose tumors precisely and systematically, and also bring the researchers of machine learning two challenges, the curse of dimensionality and the small sample size problems. We propose a manifold learning based dimensional reduction algorithm named orthogonal local discriminant embedding (O-LDE) and apply it to tumor classification. Comparing with the classical local discriminant embedding (LDE), O-LDE aims to obtain an orthogonal linear projection matrix by solving an optimization problem. After being projected into a low-dimensional subspace by O-LDE, the data points of the same class maintain their intrinsic neighbor relations, whereas the neighboring points of the different classes are far from each other. Experimental results on a public tumor dataset validate the effectiveness and feasibility of the proposed algorithm.

  16. Noniterative Design of 2-Channel FIR Orthogonal Filters

    Directory of Open Access Journals (Sweden)

    Jiménez M Elena Domínguez


    Full Text Available This paper addresses the problem of obtaining an explicit expression of all real FIR paraunitary filters. In this work, we present a general parameterization of 2-channel FIR orthogonal filters. Unlike other approaches which make use of a lattice structure, we show that our technique designs any orthogonal filter directly, with no need of iteration procedures. Moreover, in order to design an -tap 2-channel paraunitary filterbank, it suffices to choose independent parameters, and introduce them in a simple expression which provides the filter coefficients directly. Some examples illustrate how this new approach can be used for designing filters with certain desired properties. Further conditions can be eventually imposed on the parameters so as to design filters for specific applications.

  17. Stabilized Stepwise Orthogonal Matching Pursuit for Sparse Signal Approximation (United States)

    Wang, Mingjiang; Liu, Guanghong; De, Zhang; Han, Kuoye; Chen, Yanmin


    Orthogonal Matching Pursuit (OMP) algorithm is equipped with the capability to decompose any signal into a linear expansion of waveforms, which are selected from a redundant functional dictionary. Nevertheless, classical OMP algorithm suffers a heavy computational burden due to its single element selection strategy in each repetition. Recently, an accelerated implementation called stage wise orthogonal matching pursuit (StOMP) algorithm has been proposed through exploiting a multiple elements selection scheme based on an iterative threshold. However, as the defined threshold is a function of an empirical and undetermined parameter, such a reconstruction scheme is not optimal and the algorithm may get obstructed in some specific conditions. This manuscript presents an adaptive threshold selection strategy which takes signal structure into consideration and furthermore, a regularized iterative framework for sparse signal approximation is suggested. Compared with classical StOMP approach, these efforts can provide robust and more attractive approximation performance for sparse signal recoveries. Experimental results present the substantial improvements of these optimizations.

  18. Orthogonal Analysis Based Performance Optimization for Vertical Axis Wind Turbine

    Directory of Open Access Journals (Sweden)

    Lei Song


    Full Text Available Geometrical shape of a vertical axis wind turbine (VAWT is composed of multiple structural parameters. Since there are interactions among the structural parameters, traditional research approaches, which usually focus on one parameter at a time, cannot obtain performance of the wind turbine accurately. In order to exploit overall effect of a novel VAWT, we firstly use a single parameter optimization method to obtain optimal values of the structural parameters, respectively, by Computational Fluid Dynamics (CFD method; based on the results, we then use an orthogonal analysis method to investigate the influence of interactions of the structural parameters on performance of the wind turbine and to obtain optimization combination of the structural parameters considering the interactions. Results of analysis of variance indicate that interactions among the structural parameters have influence on performance of the wind turbine, and optimization results based on orthogonal analysis have higher wind energy utilization than that of traditional research approaches.

  19. Quantum secret sharing using orthogonal multiqudit entangled states (United States)

    Bai, Chen-Ming; Li, Zhi-Hui; Liu, Cheng-Ji; Li, Yong-Ming


    In this work, we investigate the distinguishability of orthogonal multiqudit entangled states under restricted local operations and classical communication. According to these properties, we propose a quantum secret sharing scheme to realize three types of access structures, i.e., the ( n, n)-threshold, the restricted (3, n)-threshold and restricted (4, n)-threshold schemes (called LOCC-QSS scheme). All cooperating players in the restricted threshold schemes are from two disjoint groups. In the proposed protocol, the participants use the computational basis measurement and classical communication to distinguish between those orthogonal states and reconstruct the original secret. Furthermore, we also analyze the security of our scheme in four primary quantum attacks and give a simple encoding method in order to better prevent the participant conspiracy attack.

  20. Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae (United States)

    Dembowski, Jill A.; Ramesh, Madhumitha; McManus, C. Joel; Woolford, John L.


    Eukaryotic ribosome assembly requires over 200 assembly factors that facilitate rRNA folding, ribosomal protein binding, and pre-rRNA processing. One such factor is Rlp7, an essential RNA binding protein required for consecutive pre-rRNA processing steps for assembly of yeast 60S ribosomal subunits: exonucleolytic processing of 27SA3 pre-rRNA to generate the 5′ end of 5.8S rRNA and endonucleolytic cleavage of the 27SB pre-rRNA to initiate removal of internal transcribed spacer 2 (ITS2). To better understand the functions of Rlp7 in 27S pre-rRNA processing steps, we identified where it crosslinks to pre-rRNA. We found that Rlp7 binds at the junction of ITS2 and the ITS2-proximal stem, between the 3′ end of 5.8S rRNA and the 5′ end of 25S rRNA. Consistent with Rlp7 binding to this neighborhood during assembly, two-hybrid and affinity copurification assays showed that Rlp7 interacts with other assembly factors that bind to or near ITS2 and the proximal stem. We used in vivo RNA structure probing to demonstrate that the proximal stem forms prior to Rlp7 binding and that Rlp7 binding induces RNA conformational changes in ITS2 that may chaperone rRNA folding and regulate 27S pre-rRNA processing. Our findings contradict the hypothesis that Rlp7 functions as a placeholder for ribosomal protein L7, from which Rlp7 is thought to have evolved in yeast. The binding site of Rlp7 is within eukaryotic-specific RNA elements, which are not found in bacteria. Thus, we propose that Rlp7 coevolved with these RNA elements to facilitate eukaryotic-specific functions in ribosome assembly and pre-rRNA processing. PMID:24129494

  1. Dynamically orthogonal field equations for stochastic flows and particle dynamics (United States)


    hypotheses on the spectrum of the orthogonal complement of the stochastic subspace. Note that we restrict ourselves to the ‘internal’ adaptation, i.e...square sense ([87]). For the case where the integrands are deterministic the mean square integral is reduced to the 40 classical Riemann integral. In...exact, closed set of equa- tions that determine the evolution of continuous stochastic fields described by a SPDE. By hypothesizing a finite order

  2. Orthogonal frequency division multiple access fundamentals and applications

    CERN Document Server

    Jiang, Tao; Zhang, Yan


    Supported by the expert-level advice of pioneering researchers, Orthogonal Frequency Division Multiple Access Fundamentals and Applications provides a comprehensive and accessible introduction to the foundations and applications of one of the most promising access technologies for current and future wireless networks. It includes authoritative coverage of the history, fundamental principles, key techniques, and critical design issues of OFDM systems. Covering various techniques of effective resource management for OFDM/OFDMA-based wireless communication systems, this cutting-edge reference:Add

  3. Superstability of the generalized orthogonality equation on restricted ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    (n ≥ 2) satisfies the functional inequality. ||〈f (x), f (y)〉| − |〈x,y〉|| ≤ ε for some ε ≥ 0 and for all x,y ∈ Rn. , then f is a solution of the generalized orthogonality equation (1). We will refer the reader to [3,6,8,12] for detailed definitions of stability and superstability of functional equations. By using ideas of Skof and Rassias [8,11], ...

  4. Orthogonal Fabry-Pérot sensors for photoacoustic tomography (United States)

    Ellwood, R.; Ogunlade, O.; Zhang, E. Z.; Beard, P. C.; Cox, B. T.


    Fabry-Pérot (FP) sensors have been used to produce in-vivo photoacoustic images of exquisite quality. However, for simplicity of construction FP sensors are produced in a planar form. Planar sensors suffer from a limited detection aperture, due to their planarity. We present a novel sensor geometry that allowed a greater field of view by placing a second sensor orthogonal to the first. This captured data from the deeper lying regions of interest and mitigated the limited view.

  5. Discrete Orthogonal Transforms and Neural Networks for Image Interpolation

    Directory of Open Access Journals (Sweden)

    J. Polec


    Full Text Available In this contribution we present transform and neural network approaches to the interpolation of images. From transform point of view, the principles from [1] are modified for 1st and 2nd order interpolation. We present several new interpolation discrete orthogonal transforms. From neural network point of view, we present interpolation possibilities of multilayer perceptrons. We use various configurations of neural networks for 1st and 2nd order interpolation. The results are compared by means of tables.

  6. Reliable exterior orientation by a robust anisotropic orthogonal Procrustes Algorithm


    Fusiello, A; Maset, E; Crosilla, F


    The paper presents a robust version of a recent anisotropic orthogonal Procrustes algorithm that has been proposed to solve the socalled camera exterior orientation problem in computer vision and photogrammetry. In order to identify outliers, that are common in visual data, we propose an algorithm based on Least Median of Squares to detect a minimal outliers-free sample, and a Forward Search procedure, used to augment the inliers set one sample at a time. Experiments with synthetic d...

  7. Structure of the chloroplast ribosome: novel domains for translation regulation.

    Directory of Open Access Journals (Sweden)

    Andrea L Manuell


    Full Text Available Gene expression in chloroplasts is controlled primarily through the regulation of translation. This regulation allows coordinate expression between the plastid and nuclear genomes, and is responsive to environmental conditions. Despite common ancestry with bacterial translation, chloroplast translation is more complex and involves positive regulatory mRNA elements and a host of requisite protein translation factors that do not have counterparts in bacteria. Previous proteomic analyses of the chloroplast ribosome identified a significant number of chloroplast-unique ribosomal proteins that expand upon a basic bacterial 70S-like composition. In this study, cryo-electron microscopy and single-particle reconstruction were used to calculate the structure of the chloroplast ribosome to a resolution of 15.5 A. Chloroplast-unique proteins are visualized as novel structural additions to a basic bacterial ribosome core. These structures are located at optimal positions on the chloroplast ribosome for interaction with mRNAs during translation initiation. Visualization of these chloroplast-unique structures on the ribosome, combined with mRNA cross-linking, allows us to propose a model for translation initiation in chloroplasts in which chloroplast-unique ribosomal proteins interact with plastid-specific translation factors and RNA elements to facilitate regulated translation of chloroplast mRNAs.

  8. PURE ribosome display and its application in antibody technology. (United States)

    Kanamori, Takashi; Fujino, Yasuhiro; Ueda, Takuya


    Ribosome display utilizes formation of the mRNA-ribosome-polypeptide ternary complex in a cell-free protein synthesis system to link genotype (mRNA) to phenotype (polypeptide). However, the presence of intrinsic components, such as nucleases in the cell-extract-based cell-free protein synthesis system, reduces the stability of the ternary complex, which would prevent attainment of reliable results. We have developed an efficient and highly controllable ribosome display system using the PURE (Protein synthesis Using Recombinant Elements) system. The mRNA-ribosome-polypeptide ternary complex is highly stable in the PURE system, and the selected mRNA can be easily recovered because activities of nucleases and other inhibitory factors are very low in the PURE system. We have applied the PURE ribosome display to antibody engineering approaches, such as epitope mapping and affinity maturation of antibodies, and obtained results showing that the PURE ribosome display is more efficient than the conventional method. We believe that the PURE ribosome display can contribute to the development of useful antibodies. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Modular and Orthogonal Synthesis of Hybrid Polymers and Networks (United States)

    Liu, Shuang; Dicker, Kevin T.; Jia, Xinqiao


    Biomaterials scientists strive to develop polymeric materials with distinct chemical make-up, complex molecular architectures, robust mechanical properties and defined biological functions by drawing inspirations from biological systems. Salient features of biological designs include (1) repetitive presentation of basic motifs; and (2) efficient integration of diverse building blocks. Thus, an appealing approach to biomaterials synthesis is to combine synthetic and natural building blocks in a modular fashion employing novel chemical methods. Over the past decade, orthogonal chemistries have become powerful enabling tools for the modular synthesis of advanced biomaterials. These reactions require building blocks with complementary functionalities, occur under mild conditions in the presence of biological molecules and living cells and proceed with high yield and exceptional selectivity. These chemistries have facilitated the construction of complex polymers and networks in a step-growth fashion, allowing facile modulation of materials properties by simple variations of the building blocks. In this review, we first summarize features of several types of orthogonal chemistries. We then discuss recent progress in the synthesis of step growth linear polymers, dendrimers and networks that find application in drug delivery, 3D cell culture and tissue engineering. Overall, orthogonal reactions and modulular synthesis have not only minimized the steps needed for the desired chemical transformations but also maximized the diversity and functionality of the final products. The modular nature of the design, combined with the potential synergistic effect of the hybrid system, will likely result in novel hydrogel matrices with robust structures and defined functions. PMID:25572255

  10. Efficiency Improvements of Antenna Optimization Using Orthogonal Fractional Experiments

    Directory of Open Access Journals (Sweden)

    Yen-Sheng Chen


    Full Text Available This paper presents an extremely efficient method for antenna design and optimization. Traditionally, antenna optimization relies on nature-inspired heuristic algorithms, which are time-consuming due to their blind-search nature. In contrast, design of experiments (DOE uses a completely different framework from heuristic algorithms, reducing the design cycle by formulating the surrogates of a design problem. However, the number of required simulations grows exponentially if a full factorial design is used. In this paper, a much more efficient technique is presented to achieve substantial time savings. By using orthogonal fractional experiments, only a small subset of the full factorial design is required, yet the resultant response surface models are still effective. The capability of orthogonal fractional experiments is demonstrated through three examples, including two tag antennas for radio-frequency identification (RFID applications and one internal antenna for long-term-evolution (LTE handheld devices. In these examples, orthogonal fractional experiments greatly improve the efficiency of DOE, thereby facilitating the antenna design with less simulation runs.

  11. Limited-memory adaptive snapshot selection for proper orthogonal decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Oxberry, Geoffrey M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kostova-Vassilevska, Tanya [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Arrighi, Bill [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chand, Kyle [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    Reduced order models are useful for accelerating simulations in many-query contexts, such as optimization, uncertainty quantification, and sensitivity analysis. However, offline training of reduced order models can have prohibitively expensive memory and floating-point operation costs in high-performance computing applications, where memory per core is limited. To overcome this limitation for proper orthogonal decomposition, we propose a novel adaptive selection method for snapshots in time that limits offline training costs by selecting snapshots according an error control mechanism similar to that found in adaptive time-stepping ordinary differential equation solvers. The error estimator used in this work is related to theory bounding the approximation error in time of proper orthogonal decomposition-based reduced order models, and memory usage is minimized by computing the singular value decomposition using a single-pass incremental algorithm. Results for a viscous Burgers’ test problem demonstrate convergence in the limit as the algorithm error tolerances go to zero; in this limit, the full order model is recovered to within discretization error. The resulting method can be used on supercomputers to generate proper orthogonal decomposition-based reduced order models, or as a subroutine within hyperreduction algorithms that require taking snapshots in time, or within greedy algorithms for sampling parameter space.

  12. A matrix Rodrigues formula for classical orthogonal polynomials in two variables


    Álvarez de Morales, María; Fernández, Lidia; Pérez, Teresa E.; Piñar, Miguel A.


    Classical orthogonal polynomials in one variable can be characterized as the only orthogonal polynomials satisfying a Rodrigues formula. In this paper, using the second kind Kronecker power of a matrix, a Rodrigues formula is introduced for classical orthogonal polynomials in two variables.

  13. The evolvability of programmable hardware (United States)

    Raman, Karthik; Wagner, Andreas


    In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected ‘neutral networks’ in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 1045 logic circuits (‘genotypes’) and 1019 logic functions (‘phenotypes’). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry. PMID:20534598

  14. The 'E' factor -- evolving endodontics. (United States)

    Hunter, M J


    Endodontics is a constantly developing field, with new instruments, preparation techniques and sealants competing with trusted and traditional approaches to tooth restoration. Thus general dental practitioners must question and understand the significance of these developments before adopting new practices. In view of this, the aim of this article, and the associated presentation at the 2013 British Dental Conference & Exhibition, is to provide an overview of endodontic methods and constantly evolving best practice. The presentation will review current preparation techniques, comparing rotary versus reciprocation, and question current trends in restoration of the endodontically treated tooth.

  15. Nilpotent orbits and the Coulomb branch of T σ ( G) theories: special orthogonal vs orthogonal gauge group factors (United States)

    Cabrera, Santiago; Hanany, Amihay; Zhong, Zhenghao


    Coulomb branches of a set of 3 d N = 4 supersymmetric gauge theories are closures of nilpotent orbits of the algebra so(n) . From the point of view of string theory, these quantum field theories can be understood as effective gauge theories describing the low energy dynamics of a brane configuration with the presence of orientifold planes [1]. The presence of the orientifold planes raises the question to whether the orthogonal factors of a the gauge group are indeed orthogonal O( N ) or special orthogonal SO( N ). In order to investigate this problem, we compute the Hilbert series for the Coulomb branch of T σ (SO( n)∨) theories, utilizing the monopole formula. The results for all nilpotent orbits from so(3) to so(10) which are special and normal are presented. A new relationship between the choice of SO/O( N ) factors in the gauge group and the Lusztig's Canonical Quotient \\overline{A}(O_{λ}) of the corresponding nilpotent orbit is observed. We also provide a new way of projecting several magnetic lattices of different SO( N ) gauge group factors by the diagonal action of a Z_2 group.

  16. Crushed rephased orthogonal slice selection (CROSS) for simultaneous acquisition of two orthogonal proton resonance frequency temperature maps. (United States)

    Krafft, Axel J; Rauschenberg, Jaane; Maier, Florian; Jenne, Jürgen W; Bock, Michael


    To evaluate a novel imaging sequence termed crushed rephased orthogonal slice selection (CROSS) that uses the available time in long echo time (TE) gradient echo (GRE) imaging-as employed for proton resonance frequency (PRF) shift thermometry-to simultaneously acquire two orthogonal magnetic resonance imaging (MRI) temperature maps around the target region. The CROSS sequence encodes a second orthogonal slice between excitation and data readout in long-TE imaging and applies dedicated crusher (CR) gradients to separate the signals from the two slices. Numerical simulations of the Bloch equations and phantom experiments were performed to analyze the MR signal. In phantom and in vivo experiments with two domestic pigs, the applicability of the CROSS sequence for temperature mapping of thermal therapies with focused ultrasound and laser was studied. A successful separation of the signals from the two slices was achieved for CR dephasing lengths approaching the in-plane resolution. In the two animal experiments, CROSS temperature mapping could be successfully demonstrated at a temporal resolution of 2-3 seconds and a temperature uncertainty of 3-4K. At the expense of a reduced signal in the overlap of the two slices, the CROSS sequence achieves an improvement of temporal resolution by 50%, without requiring further acceleration techniques such as parallel imaging, over conventional sequential GRE sequences employing the same repetition time as the CROSS sequence acquires two slices within one repetition interval. Copyright © 2013 Wiley Periodicals, Inc.

  17. Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins

    Directory of Open Access Journals (Sweden)

    Gayani N. P. Dedduwa-Mudalige


    Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.

  18. A process yields large quantities of pure ribosome subunits (United States)

    Friedman, M.; Lu, P.; Rich, A.


    Development of process for in-vitro protein synthesis from living cells followed by dissociation of ribosomes into subunits is discussed. Process depends on dialysis or use of chelating agents. Operation of process and advantages over previous methods are outlined.

  19. Crystal structures of ribosome anti-association factor IF6. (United States)

    Groft, C M; Beckmann, R; Sali, A; Burley, S K


    Ribosome anti-association factor eIF6 (originally named according to translation initiation terminology as eukaryotic initiation factor 6) binds to the large ribosomal subunit, thereby preventing inappropriate interactions with the small subunit during initiation of protein synthesis. We have determined the X-ray structures of two IF6 homologs, Methanococcus jannaschii archaeal aIF6 and Sacchromyces cerevisiae eIF6, revealing a phylogenetically conserved 25 kDa protein consisting of five quasi identical alpha/beta subdomains arrayed about a five-fold axis of pseudosymmetry. Yeast eIF6 prevents ribosomal subunit association. Comparative protein structure modeling with other known archaeal and eukaryotic homologs demonstrated the presence of two conserved surface regions, one or both of which may bind the large ribosomal subunit.

  20. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Linskens, Maarten H.K.; Huberman, Joel A.


    Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

  1. Structure of plant nuclear and ribosomal DNA containing chromatin. (United States)

    Leber, B; Hemleben, V


    Digestion of plant chromatin from Brassica pekinensis and Matthiola incana with staphylococcus nuclease leads to a DNA repeat of 175 plus or minus 8 and a core size of 140 base pairs. DNase I digestion results in multiples of 10 bases. Ribosomal RNN genes were studied as a model system for active plant chromatin because of their great redundancy and their high transcriptional activity in growing and differentiating tissues. The actively transcribed genes were identified by nascent RNA of ribosomal origin still attached to its matrix DNA. Hybridization techniques were used to demonstrate that even transcriptionally active gene sequences are present in nuclease generated chromatin subunits. Comparison of the DNase I kinetics of chromatin digestion with the amount of ribosomal RNA genes which is available for hybridization at the given times indicated that ribosomal RNA genes are digested, but not preferentially degraded by DNase I.

  2. Revising the taxonomic distribution, origin and evolution of ribosome inactivating protein genes.

    Directory of Open Access Journals (Sweden)

    Walter J Lapadula

    Full Text Available Ribosome inactivating proteins are enzymes that depurinate a specific adenine residue in the alpha-sarcin-ricin loop of the large ribosomal RNA, being ricin and Shiga toxins the most renowned examples. They are widely distributed in plants and their presence has also been confirmed in a few bacterial species. According to this taxonomic distribution, the current model about the origin and evolution of RIP genes postulates that an ancestral RIP domain was originated in flowering plants, and later acquired by some bacteria via horizontal gene transfer. Here, we unequivocally detected the presence of RIP genes in fungi and metazoa. These findings, along with sequence and phylogenetic analyses, led us to propose an alternative, more parsimonious, hypothesis about the origin and evolutionary history of the RIP domain, where several paralogous RIP genes were already present before the three domains of life evolved. This model is in agreement with the current idea of the Last Universal Common Ancestor (LUCA as a complex, genetically redundant organism. Differential loss of paralogous genes in descendants of LUCA, rather than multiple horizontal gene transfer events, could account for the complex pattern of RIP genes across extant species, as it has been observed for other genes.

  3. The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes. (United States)

    Hendriks, L; Van de Peer, Y; Van Herck, M; Neefs, J M; De Wachter, R


    Evolutionary trees based on partial small ribosomal subunit RNA sequences of 22 metazoa species have been published [(1988) Science 239, 748-753]. In these trees, cnidarians (Radiata) seemed to have evolved independently from the Bilateria, which is in contradiction with the general evolutionary view. In order to further investigate this problem, the complete srRNA sequence of the sea anemone Anemonia sulcata was determined and evolutionary trees were constructed using a matrix optimization method. In the tree thus obtained the sea anemone and Bilateria together form a monophyletic cluster, with the sea anemone forming the first line of the metazoan group.

  4. Orthogonal projection of points in CAD/CAM applications: an overview

    Directory of Open Access Journals (Sweden)

    Kwanghee Ko


    Full Text Available This paper aims to review methods for computing orthogonal projection of points onto curves and surfaces, which are given in implicit or parametric form or as point clouds. Special emphasis is place on orthogonal projection onto conics along with reviews on orthogonal projection of points onto curves and surfaces in implicit and parametric form. Except for conics, computation methods are classified into two groups based on the core approaches: iterative and subdivision based. An extension of orthogonal projection of points to orthogonal projection of curves onto surfaces is briefly explored. Next, the discussion continues toward orthogonal projection of points onto point clouds, which spawns a different branch of algorithms in the context of orthogonal projection. The paper concludes with comments on guidance for an appropriate choice of methods for various applications.

  5. Bi-orthogonal Symbol Mapping and Detection in Optical CDMA Communication System (United States)

    Liu, Maw-Yang


    In this paper, the bi-orthogonal symbol mapping and detection scheme is investigated in time-spreading wavelength-hopping optical CDMA communication system. The carrier-hopping prime code is exploited as signature sequence, whose put-of-phase autocorrelation is zero. Based on the orthogonality of carrier-hopping prime code, the equal weight orthogonal signaling scheme can be constructed, and the proposed scheme using bi-orthogonal symbol mapping and detection can be developed. The transmitted binary data bits are mapped into corresponding bi-orthogonal symbols, where the orthogonal matrix code and its complement are utilized. In the receiver, the received bi-orthogonal data symbol is fed into the maximum likelihood decoder for detection. Under such symbol mapping and detection, the proposed scheme can greatly enlarge the Euclidean distance; hence, the system performance can be drastically improved.

  6. Ribosome heterogeneity in tumorigenesis: the rRNA point of view


    Marcel, Virginie; Catez, Fr?d?ric; Diaz, Jean-Jacques


    The "specialized ribosome" concept proposes that ribosome variants are produced and differentially regulate translation. Examples supporting this notion demonstrated heterogeneity of ribosomal protein composition. However, ribosome translational activity is carried out by rRNA. We, and others, recently showed that rRNA heterogeneity regulates translation to generate distinct translatomes promoting tumorigenesis.

  7. Interaction of Pleuromutilin Derivatives with the Ribosomal Peptidyl Transferase Center


    Long, Katherine S.; Hansen, Lykke H.; Jakobsen, Lene; Vester, Birte


    Tiamulin is a pleuromutilin antibiotic that is used in veterinary medicine. The recently published crystal structure of a tiamulin-50S ribosomal subunit complex provides detailed information about how this drug targets the peptidyl transferase center of the ribosome. To promote rational design of pleuromutilin-based drugs, the binding of the antibiotic pleuromutilin and three semisynthetic derivatives with different side chain extensions has been investigated using chemical footprinting. The ...

  8. Comparison of genes fragments coding for ribosomal protein in sugarcane

    Directory of Open Access Journals (Sweden)

    María I. Oloriz


    Full Text Available Partial sequences of sugarcane genes, obtained by means of a subtractive library were identified by BLAST alignment against all sequences available in the databases. During the homology search, five genes were identified as chloroplast or citosol ribosomal proteins. The biggest homology obtained among the identified sequences as ribosomal proteins of sugarcane was with the corn genome. Key words: consensus domain, Saccharum spp., subtractive library

  9. Primordial evolvability: Impasses and challenges. (United States)

    Vasas, Vera; Fernando, Chrisantha; Szilágyi, András; Zachár, István; Santos, Mauro; Szathmáry, Eörs


    While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of

  10. Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer. (United States)

    Lapadula, Walter J; Marcet, Paula L; Mascotti, María L; Sanchez-Puerta, M Virginia; Juri Ayub, Maximiliano


    Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms.

  11. Bayesian prediction of RNA translation from ribosome profiling. (United States)

    Malone, Brandon; Atanassov, Ilian; Aeschimann, Florian; Li, Xinping; Großhans, Helge; Dieterich, Christoph


    Ribosome profiling via high-throughput sequencing (ribo-seq) is a promising new technique for characterizing the occupancy of ribosomes on messenger RNA (mRNA) at base-pair resolution. The ribosome is responsible for translating mRNA into proteins, so information about its occupancy offers a detailed view of ribosome density and position which could be used to discover new translated open reading frames (ORFs), among other things. In this work, we propose Rp-Bp, an unsupervised Bayesian approach to predict translated ORFs from ribosome profiles. We use state-of-the-art Markov chain Monte Carlo techniques to estimate posterior distributions of the likelihood of translation of each ORF. Hence, an important feature of Rp-Bp is its ability to incorporate and propagate uncertainty in the prediction process. A second novel contribution is automatic Bayesian selection of read lengths and ribosome P-site offsets (BPPS). We empirically demonstrate that our read length selection technique modestly improves sensitivity by identifying more canonical and non-canonical ORFs. Proteomics- and quantitative translation initiation sequencing-based validation verifies the high quality of all of the predictions. Experimental comparison shows that Rp-Bp results in more peptide identifications and proteomics-validated ORF predictions compared to another recent tool for translation prediction. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Dual effect of chloramphenicol peptides on ribosome inhibition. (United States)

    Bougas, Anthony; Vlachogiannis, Ioannis A; Gatos, Dimitrios; Arenz, Stefan; Dinos, George P


    Chloramphenicol peptides were recently established as useful tools for probing nascent polypeptide chain interaction with the ribosome, either biochemically, or structurally. Here, we present a new 10mer chloramphenicol peptide, which exerts a dual inhibition effect on the ribosome function affecting two distinct areas of the ribosome, namely the peptidyl transferase center and the polypeptide exit tunnel. According to our data, the chloramphenicol peptide bound on the chloramphenicol binding site inhibits the formation of both acetyl-phenylalanine-puromycin and acetyl-lysine-puromycin, showing, however, a decreased peptidyl transferase inhibition compared to chloramphenicol-mediated inhibition per se. Additionally, we found that the same compound is a strong inhibitor of green fluorescent protein synthesis in a coupled in vitro transcription-translation assay as well as a potent inhibitor of lysine polymerization in a poly(A)-programmed ribosome, showing that an additional inhibitory effect may exist. Since chemical protection data supported the interaction of the antibiotic with bases A2058 and A2059 near the entrance of the tunnel, we concluded that the extra inhibition effect on the synthesis of longer peptides is coming from interactions of the peptide moiety of the drug with residues comprising the ribosomal tunnel, and by filling up the tunnel and blocking nascent chain progression through the restricted tunnel. Therefore, the dual interaction of the chloramphenicol peptide with the ribosome increases its inhibitory effect and opens a new window for improving the antimicrobial potency of classical antibiotics or designing new ones.

  13. Peripartum hysterectomy: an evolving picture.

    LENUS (Irish Health Repository)

    Turner, Michael J


    Peripartum hysterectomy (PH) is one of the obstetric catastrophes. Evidence is emerging that the role of PH in modern obstetrics is evolving. Improving management of postpartum hemorrhage and newer surgical techniques should decrease PH for uterine atony. Rising levels of repeat elective cesarean deliveries should decrease PH following uterine scar rupture in labor. Increasing cesarean rates, however, have led to an increase in the number of PHs for morbidly adherent placenta. In the case of uterine atony or rupture where PH is required, a subtotal PH is often sufficient. In the case of pathological placental localization involving the cervix, however, a total hysterectomy is required. Furthermore, the involvement of other pelvic structures may prospectively make the diagnosis difficult and the surgery challenging. If resources permit, PH for pathological placental localization merits a multidisciplinary approach. Despite advances in clinical practice, it is likely that peripartum hysterectomy will be more challenging for obstetricians in the future.

  14. Simple and inexpensive ribosome profiling analysis of mRNA translation. (United States)

    Reid, David W; Shenolikar, Shirish; Nicchitta, Christopher V


    The development and application of ribosome profiling has markedly advanced our understanding of ribosomes and mRNA translation. The experimental approach, which relies on deep sequencing of ribosome-protected mRNA fragments generated by treatment of polyribosomes with exogenous nucleases, provides a transcriptome-wide assessment of translation. The broad application of ribosome profiling has been slowed by the complexity and expense of the protocol. Here, we provide a simplified ribosome profiling method that uses micrococcal nuclease to generate ribosome footprints in crude cellular extracts, which are then purified simply by size selection via polyacrylamide gel electrophoresis. This simplification removes the laborious or expensive purification of ribosomes that has typically been used. This direct extraction method generates gene-level ribosome profiling data that are similar to a method that includes ribosome purification. This protocol should significantly ease the barrier to entry for research groups interested in employing ribosome profiling. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy. (United States)

    Kato, Takayuki; Yoshida, Hideji; Miyata, Tomoko; Maki, Yasushi; Wada, Akira; Namba, Keiichi


    In the stationary growth phase of bacteria, protein biosynthesis on ribosomes is suppressed, and the ribosomes are preserved in the cell by the formation of the 100S ribosome. The 100S ribosome is a dimer of the 70S ribosome and is formed by the binding of the ribosome modulation factor and the hibernation promoting factor. However, the binding mode between the two 70S ribosomes and the mechanism of complex formation are still poorly understood. Here, we report the structure of the 100S ribosome by electron cryomicroscopy and single-particle image analysis. The 100S ribosome purified from the cell in the stationary growth phase is composed of two transfer RNA-free 70S ribosomes, has two-fold symmetry, and is formed through interactions between their 30S subunits, where interactions between small subunit proteins, S2, S3 and S5, appear to be critical for the dimerization.

  16. Extreme evolved solar systems (EESS) (United States)

    Gaensicke, Boris


    In just 20 years, we went from not knowing if the solar system is a fluke of Nature to realising that it is totally normal for stars to have planets. More remarkably, it is now clear that planet formation is a robust process, as rich multi-planet systems are found around stars more massive and less massive than the Sun. More recently, planetary systems have been identified in increasingly complex architectures, including circumbinary planets, wide binaries with planets orbiting one or both stellar components, and planets in triple stellar systems.We have also learned that many planetary systems will survive the evolution of their host stars into the white dwarf phase. Small bodies are scattered by unseen planets into the gravitational field of the white dwarfs, tidally disrupt, form dust discs, and eventually accrete onto the white dwarf, where they can be spectroscopically detected. HST/COS has played a critical role in the study these evolved planetary systems, demonstrating that overall the bulk composition of the debris is rocky and resembles in composition the inner the solar system, including evidence for water-rich planetesimals. Past observations of planetary systems at white dwarfs have focused on single stars with main-sequence progenitors of 1.5 to 2.5Msun. Here we propose to take the study of evolved planetary systems into the extremes of parameter ranges to answer questions such as: * How efficient is planet formation around 4-10Msun stars? * What are the metallicities of the progenitors of debris-accreting white dwarfs?* What is the fate of circumbinary planets?* Can star-planet interactions generate magnetic fields in the white dwarf host?

  17. Adaptive PID control based on orthogonal endocrine neural networks. (United States)

    Milovanović, Miroslav B; Antić, Dragan S; Milojković, Marko T; Nikolić, Saša S; Perić, Staniša Lj; Spasić, Miodrag D


    A new intelligent hybrid structure used for online tuning of a PID controller is proposed in this paper. The structure is based on two adaptive neural networks, both with built-in Chebyshev orthogonal polynomials. First substructure network is a regular orthogonal neural network with implemented artificial endocrine factor (OENN), in the form of environmental stimuli, to its weights. It is used for approximation of control signals and for processing system deviation/disturbance signals which are introduced in the form of environmental stimuli. The output values of OENN are used to calculate artificial environmental stimuli (AES), which represent required adaptation measure of a second network-orthogonal endocrine adaptive neuro-fuzzy inference system (OEANFIS). OEANFIS is used to process control, output and error signals of a system and to generate adjustable values of proportional, derivative, and integral parameters, used for online tuning of a PID controller. The developed structure is experimentally tested on a laboratory model of the 3D crane system in terms of analysing tracking performances and deviation signals (error signals) of a payload. OENN-OEANFIS performances are compared with traditional PID and 6 intelligent PID type controllers. Tracking performance comparisons (in transient and steady-state period) showed that the proposed adaptive controller possesses performances within the range of other tested controllers. The main contribution of OENN-OEANFIS structure is significant minimization of deviation signals (17%-79%) compared to other controllers. It is recommended to exploit it when dealing with a highly nonlinear system which operates in the presence of undesirable disturbances. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Directed Formation of DNA Nanoarrays through Orthogonal Self-Assembly

    Directory of Open Access Journals (Sweden)

    Eugen Stulz


    Full Text Available We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II and Ni(II induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.

  19. A turbulent jet in crossflow analysed with proper orthogonal decomposition

    DEFF Research Database (Denmark)

    Meyer, Knud Erik; Pedersen, Jakob Martin; Özcan, Oktay


    and that they interact strongly with the jet core. The analysis identifies jet shear-layer vortices and finds that these vortical structures are more local and thus less dominant. For R = 1.3, on the other hand, jet shear-layer vortices are the most dominant, while the wake vortices are much less important. For both...... and pipe diameter was 2400 and the jet to crossflow velocity ratios were R = 3.3 and R = 1.3. The experimental data have been analysed by proper orthogonal decomposition (POD). For R = 3.3, the results in several different planes indicate that the wake vortices are the dominant dynamic flow structures...

  20. Discrete phase-space approach to mutually orthogonal Latin squares (United States)

    Gaeta, Mario; Di Matteo, Olivia; Klimov, Andrei B.; de Guise, Hubert


    We show there is a natural connection between Latin squares and commutative sets of monomials defining geometric structures in finite phase-space of prime power dimensions. A complete set of such monomials defines a mutually unbiased basis (MUB) and may be associated with a complete set of mutually orthogonal Latin squares (MOLS). We translate some possible operations on the monomial sets into isomorphisms of Latin squares, and find a general form of permutations that map between Latin squares corresponding to unitarily equivalent mutually unbiased sets.

  1. Neural Based Orthogonal Data Fitting The EXIN Neural Networks

    CERN Document Server

    Cirrincione, Giansalvo


    Written by three leaders in the field of neural based algorithms, Neural Based Orthogonal Data Fitting proposes several neural networks, all endowed with a complete theory which not only explains their behavior, but also compares them with the existing neural and traditional algorithms. The algorithms are studied from different points of view, including: as a differential geometry problem, as a dynamic problem, as a stochastic problem, and as a numerical problem. All algorithms have also been analyzed on real time problems (large dimensional data matrices) and have shown accurate solutions. Wh

  2. Orthogonal polarization in lasers physical phenomena and engineering applications

    CERN Document Server

    Zhang, Shulian


    This practical book summarizes the latest research results of orthogonally polarized lasers, birefringence laser cavities, and their applications. Coverage ranges from basic principles and technologies to the characteristics of different cavities and lasers to various measurement techniques. A number of figures, experimental designs, and measurement curves are included, helping readers gain a thorough understanding of the many applications in modern engineering and start their own projects. Many types of relevant lasers (Helium/Neon lasers, Nd:YAG lasers, laser diodes, etc.) are also discussed

  3. The endoscopic classification of representations orthogonal and symplectic groups

    CERN Document Server

    Arthur, James


    Within the Langlands program, endoscopy is a fundamental process for relating automorphic representations of one group with those of another. In this book, Arthur establishes an endoscopic classification of automorphic representations of orthogonal and symplectic groups G. The representations are shown to occur in families (known as global L-packets and A-packets), which are parametrized by certain self-dual automorphic representations of an associated general linear group GL(N). The central result is a simple and explicit formula for the multiplicity in the automorphic discrete spectrum of G

  4. Orthogonal frequency division multiplexing simulation based on MATLAB (United States)

    Qiao, Yuan


    OFDM (Orthogonal Frequency Division Multiplexing) is one of the core technologies in the fourth generation mobile communication system. It is a widely-used method of the multi-carrier modulations based on IFFT and FFT transform, it can achieve the lowest complexity and effectively combat frequency selective fading. In this paper, we successfully use MATLAB to do the simulation of OFDM, and obtained good results, in which successful recovery out of the original signal under real channel condition, and error is less than 5% with the original signal.

  5. Synthesis of an Orthogonal Topological Analogue of Helicene

    DEFF Research Database (Denmark)

    Wixe, Torbjörn; Wallentin, Carl‐Johan; Johnson, Magnus T.


    The synthesis of an orthogonal topological pentamer analogue of helicene is presented. This analogue forms a tubular structure with its aromatic systems directed parallel to the axis of propagation, which creates a cavity with the potential to function as a host molecule. The synthetic strategy...... reported, based on a series of repeating Friedländer condensations that utilize pyrido[3,2‐d]pyrimidine moieties as protected amino aldehydes, allows for the facile access of higher generations of helical, tubular structures. As a result of the synthetic strategy, only a helical isomer of the pentamer...

  6. Nucleic acid constructs containing orthogonal site selective recombinases (OSSRs)

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Joshua M.; Anderson, J. Christopher; Dueber, John E.


    The present invention provides for a recombinant nucleic acid comprising a nucleotide sequence comprising a plurality of constructs, wherein each construct independently comprises a nucleotide sequence of interest flanked by a pair of recombinase recognition sequences. Each pair of recombinase recognition sequences is recognized by a distinct recombinase. Optionally, each construct can, independently, further comprise one or more genes encoding a recombinase capable of recognizing the pair of recombinase recognition sequences of the construct. The recombinase can be an orthogonal (non-cross reacting), site-selective recombinase (OSSR).

  7. [Formulation optimization of ginkgo flavonoids matrix tablets by orthogonal design]. (United States)

    Guo, Ying-Xin; Li, Fei; Zhao, Qian-Qian; Xu, Lu; Pan, Wei-San; Xiao, Wei; Yang, Xing-Gang


    Sustained-release tablet has become one of the hottest research spots in the area of sustained release preparations with its unique advantages. At present, a series of shortcomings were exited in the ordinary ginkgo preparations, which were used for the treatment of cardiovascular and cerebrovascular diseases. In order to avoid these shortcomings, ginkgo flavonoids matrix tablets were prepared in this paper. Furthermore, the amount and varieties of matrix material, adhesives and fillers were investigated. Meanwhile, the formulation was optimized by using the method of orthogonal design, and Zero-order, First-order, Higuchi, Ritger-peppas equation were used for the model fitting and mechanism discussing of drug release.

  8. Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions (United States)

    Morelli, Eugene A.


    A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

  9. The Orthogonal Projection and the Riesz Representation Theorem

    Directory of Open Access Journals (Sweden)

    Narita Keiko


    Full Text Available In this article, the orthogonal projection and the Riesz representation theorem are mainly formalized. In the first section, we defined the norm of elements on real Hilbert spaces, and defined Mizar functor RUSp2RNSp, real normed spaces as real Hilbert spaces. By this definition, we regarded sequences of real Hilbert spaces as sequences of real normed spaces, and proved some properties of real Hilbert spaces. Furthermore, we defined the continuity and the Lipschitz the continuity of functionals on real Hilbert spaces.

  10. Photoacoustic tomography using orthogonal Fabry-Pérot sensors. (United States)

    Ellwood, Robert; Ogunlade, Olumide; Zhang, Edward; Beard, Paul; Cox, Ben


    Fabry–Pérot sensors have been used to produce in-vivo photoacoustic images of exquisite quality. However, for ease of construction and interrogation, they are produced in a planar form. Planar arrays suffer from a limited detection aperture, which leads to artifacts in the reconstruction of the initial pressure distribution. Here, an L-shaped detection geometry is described that allows a greater field of view by placing a second planar array orthogonal to the first. This captures data from the deeper lying regions of interest and mitigates the limited view, thus reducing artifacts in the reconstructed initial pressure distribution.

  11. Photoacoustic tomography using orthogonal Fabry-Pérot sensors (United States)

    Ellwood, Robert; Ogunlade, Olumide; Zhang, Edward; Beard, Paul; Cox, Ben


    Fabry-Pérot sensors have been used to produce in-vivo photoacoustic images of exquisite quality. However, for ease of construction and interrogation, they are produced in a planar form. Planar arrays suffer from a limited detection aperture, which leads to artifacts in the reconstruction of the initial pressure distribution. Here, an L-shaped detection geometry is described that allows a greater field of view by placing a second planar array orthogonal to the first. This captures data from the deeper lying regions of interest and mitigates the limited view, thus reducing artifacts in the reconstructed initial pressure distribution.

  12. Orthogonal polynomial approximation in higher dimensions: Applications in astrodynamics (United States)

    Bani Younes, Ahmad Hani Abd Alqader

    We propose novel methods to utilize orthogonal polynomial approximation in higher dimension spaces, which enable us to modify classical differential equation solvers to perform high precision, long-term orbit propagation. These methods have immediate application to efficient propagation of catalogs of Resident Space Objects (RSOs) and improved accounting for the uncertainty in the ephemeris of these objects. More fundamentally, the methodology promises to be of broad utility in solving initial and two point boundary value problems from a wide class of mathematical representations of problems arising in engineering, optimal control, physical sciences and applied mathematics. We unify and extend classical results from function approximation theory and consider their utility in astrodynamics. Least square approximation, using the classical Chebyshev polynomials as basis functions, is reviewed for discrete samples of the to-be-approximated function. We extend the orthogonal approximation ideas to n-dimensions in a novel way, through the use of array algebra and Kronecker operations. Approximation of test functions illustrates the resulting algorithms and provides insight into the errors of approximation, as well as the associated errors arising when the approximations are differentiated or integrated. Two sets of applications are considered that are challenges in astrodynamics. The first application addresses local approximation of high degree and order geopotential models, replacing the global spherical harmonic series by a family of locally precise orthogonal polynomial approximations for efficient computation. A method is introduced which adapts the approximation degree radially, compatible with the truth that the highest degree approximations (to ensure maximum acceleration error < 10-9 ms-2, globally) are required near the Earths surface, whereas lower degree approximations are required as radius increases. We show that a four order of magnitude speedup is

  13. Universality of Mesoscopic Fluctuations for Orthogonal Polynomial Ensembles (United States)

    Breuer, Jonathan; Duits, Maurice


    We prove that the fluctuations of mesoscopic linear statistics for orthogonal polynomial ensembles are universal in the sense that two measures with asymptotic recurrence coefficients have the same asymptotic mesoscopic fluctuations (under an additional assumption on the local regularity of one of the measures). The convergence rate of the recurrence coefficients determines the range of scales on which the limiting fluctuations are identical. Our main tool is an analysis of the Green's function for the associated Jacobi matrices.As a particular consequencewe obtain a central limit theorem for the modified Jacobi Unitary Ensembles on all mesoscopic scales.

  14. Conditioning Analysis of Incomplete Cholesky Factorizations with Orthogonal Dropping

    Energy Technology Data Exchange (ETDEWEB)

    Napov, Artem [Free Univ. of Brussels (Belgium)


    The analysis of preconditioners based on incomplete Cholesky factorization in which the neglected (dropped) components are orthogonal to the approximations being kept is presented. General estimate for the condition number of the preconditioned system is given which only depends on the accuracy of individual approximations. The estimate is further improved if, for instance, only the newly computed rows of the factor are modified during each approximation step. In this latter case it is further shown to be sharp. The analysis is illustrated with some existing factorizations in the context of discretized elliptic partial differential equations.

  15. Neurodegeneration-associated instability of ribosomal DNA. (United States)

    Hallgren, Justin; Pietrzak, Maciej; Rempala, Grzegorz; Nelson, Peter T; Hetman, Michal


    Homologous recombination (HR)-mediated instability of the repetitively organized ribosomal DNA (rDNA) has been proposed as a mediator of cell senescence in yeast triggering the DNA damage response. High individual variability in the content of human rDNA suggests that this genomic region remained relatively unstable throughout evolution. Therefore, quantitative real-time polymerase chain reaction was used to determine the genomic content of rDNA in post mortem samples of parietal cortex from 14 young and 9 elderly individuals with no diagnosis of a chronic neurodegenerative/neurological disease. In addition, rDNA content in that brain region was compared between 10 age-matched control individuals and 10 patients with dementia with Lewy bodies (DLB) which involves neurodegeneration of the cerebral cortex. Probing rRNA-coding regions of rDNA revealed no effects of aging on the rDNA content. Elevated rDNA content was observed in DLB. Conversely, in the DLB pathology-free cerebellum, lower genomic content of rDNA was present in the DLB group. In the parietal cortex, such a DLB-associated instability of rDNA was not accompanied by any major changes of cytosine-phosphate-guanine methylation of the rDNA promoter. As increased cerebro-cortical rDNA content was previously reported in Alzheimer's disease, neurodegeneration appears to be associated with instability of rDNA. The hypothetical origins and consequences of this phenomenon are discussed including possibilities that the DNA damage-induced recombination destabilizes rDNA and that differential content of rDNA affects heterochromatin formation, gene expression and/or DNA damage response. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Changes in chloroplastic and cytoplasmic ribosomal protein after GA3-treatment of Zea mays leaves

    Directory of Open Access Journals (Sweden)

    P. Masłowski


    Full Text Available Protein was isolated from chioroplastic and cytoplasmic ribosomes of 14-day-old maize leaves subjected to the action of gibberellic acid. The proteins were separated electrophoretically on polyacrylamide gel. Fourteen fractions of ribosomal protein were obtained exhibiting wide electrophoretic differences. Qualitative differences were found between the chloroplastic and cytoplasmic ribosomes. Gibberellic acid caused the appearance of an additional protein Traction in cytoplasmic ribosomes. It did not, however, affect the qualitative composition of ribosome proteins from chloroplasts.

  17. Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors. (United States)

    Requião, Rodrigo D; de Souza, Henrique José Araujo; Rossetto, Silvana; Domitrovic, Tatiana; Palhano, Fernando L


    It has been proposed that polybasic peptides cause slower movement of ribosomes through an electrostatic interaction with the highly negative ribosome exit tunnel. Ribosome profiling data-the sequencing of short ribosome-bound fragments of mRNA-is a powerful tool for the analysis of mRNA translation. Using the yeast Saccharomyces cerevisiae as a model, we showed that reduced translation efficiency associated with polybasic protein sequences could be inferred from ribosome profiling. However, an increase in ribosome density at polybasic sequences was evident only when the commonly used translational inhibitors cycloheximide and anisomycin were omitted during mRNA isolation. Since ribosome profiling performed without inhibitors agrees with experimental evidence obtained by other methods, we conclude that cycloheximide and anisomycin must be avoided in ribosome profiling experiments.

  18. Cerenkov luminescence tomography based on preconditioning orthogonal matching pursuit (United States)

    Liu, Haixiao; Hu, Zhenhua; Wang, Kun; Tian, Jie; Yang, Xin


    Cerenkov luminescence imaging (CLI) is a novel optical imaging method and has been proved to be a potential substitute of the traditional radionuclide imaging such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). This imaging method inherits the high sensitivity of nuclear medicine and low cost of optical molecular imaging. To obtain the depth information of the radioactive isotope, Cerenkov luminescence tomography (CLT) is established and the 3D distribution of the isotope is reconstructed. However, because of the strong absorption and scatter, the reconstruction of the CLT sources is always converted to an ill-posed linear system which is hard to be solved. In this work, the sparse nature of the light source was taken into account and the preconditioning orthogonal matching pursuit (POMP) method was established to effectively reduce the ill-posedness and obtain better reconstruction accuracy. To prove the accuracy and speed of this algorithm, a heterogeneous numerical phantom experiment and an in vivo mouse experiment were conducted. Both the simulation result and the mouse experiment showed that our reconstruction method can provide more accurate reconstruction result compared with the traditional Tikhonov regularization method and the ordinary orthogonal matching pursuit (OMP) method. Our reconstruction method will provide technical support for the biological application for Cerenkov luminescence.

  19. Orthogonal topography in the parallel input architecture of songbird HVC. (United States)

    Elliott, Kevin C; Wu, Wei; Bertram, Richard; Hyson, Richard L; Johnson, Frank


    Neural activity within the cortical premotor nucleus HVC (acronym is name) encodes the learned songs of adult male zebra finches (Taeniopygia guttata). HVC activity is driven and/or modulated by a group of five afferent nuclei (the Medial Magnocellular nucleus of the Anterior Nidopallium, MMAN; Nucleus Interface, NIf; nucleus Avalanche, Av; the Robust nucleus of the Arcopallium, RA; the Uvaeform nucleus, Uva). While earlier evidence suggested that HVC receives a uniformly distributed and nontopographic pattern of afferent input, recent evidence suggests this view is incorrect (Basista et al., ). Here, we used a double-labeling strategy (varying both the distance between and the axial orientation of dual tracer injections into HVC) to reveal a massively parallel and in some cases topographic pattern of afferent input. Afferent neurons target only one rostral or caudal location within medial or lateral HVC, and each HVC location receives convergent input from each afferent nucleus in parallel. Quantifying the distributions of single-labeled cells revealed an orthogonal topography in the organization of afferent input from MMAN and NIf, two cortical nuclei necessary for song learning. MMAN input is organized across the lateral-medial axis whereas NIf input is organized across the rostral-caudal axis. To the extent that HVC activity is influenced by afferent input during the learning, perception, or production of song, functional models of HVC activity may need revision to account for the parallel input architecture of HVC, along with the orthogonal input topography of MMAN and NIf. © 2017 Wiley Periodicals, Inc.

  20. Video Pedestrian Detection Based on Orthogonal Scene Motion Pattern

    Directory of Open Access Journals (Sweden)

    Jianming Qu


    Full Text Available In fixed video scenes, scene motion patterns can be a very useful prior knowledge for pedestrian detection which is still a challenge at present. A new approach of cascade pedestrian detection using an orthogonal scene motion pattern model in a general density video is developed in this paper. To statistically model the pedestrian motion pattern, a probability grid overlaying the whole scene is set up to partition the scene into paths and holding areas. Features extracted from different pattern areas are classified by a group of specific strategies. Instead of using a unitary classifier, the employed classifier is composed of two directional subclassifiers trained, respectively, with different samples which are selected by two orthogonal directions. Considering that the negative images from the detection window scanning are much more than the positive ones, the cascade AdaBoost technique is adopted by the subclassifiers to reduce the negative image computations. The proposed approach is proved effectively by static classification experiments and surveillance video experiments.

  1. Deep Network Based on Stacked Orthogonal Convex Incremental ELM Autoencoders

    Directory of Open Access Journals (Sweden)

    Chao Wang


    Full Text Available Extreme learning machine (ELM as an emerging technology has recently attracted many researchers’ interest due to its fast learning speed and state-of-the-art generalization ability in the implementation. Meanwhile, the incremental extreme learning machine (I-ELM based on incremental learning algorithm was proposed which outperforms many popular learning algorithms. However, the incremental algorithms with ELM do not recalculate the output weights of all the existing nodes when a new node is added and cannot obtain the least-squares solution of output weight vectors. In this paper, we propose orthogonal convex incremental learning machine (OCI-ELM with Gram-Schmidt orthogonalization method and Barron’s convex optimization learning method to solve the nonconvex optimization problem and least-squares solution problem, and then we give the rigorous proofs in theory. Moreover, in this paper, we propose a deep architecture based on stacked OCI-ELM autoencoders according to stacked generalization philosophy for solving large and complex data problems. The experimental results verified with both UCI datasets and large datasets demonstrate that the deep network based on stacked OCI-ELM autoencoders (DOC-IELM-AEs outperforms the other methods mentioned in the paper with better performance on regression and classification problems.

  2. An Orthogonal Evolutionary Algorithm With Learning Automata for Multiobjective Optimization. (United States)

    Dai, Cai; Wang, Yuping; Ye, Miao; Xue, Xingsi; Liu, Hailin


    Research on multiobjective optimization problems becomes one of the hottest topics of intelligent computation. In order to improve the search efficiency of an evolutionary algorithm and maintain the diversity of solutions, in this paper, the learning automata (LA) is first used for quantization orthogonal crossover (QOX), and a new fitness function based on decomposition is proposed to achieve these two purposes. Based on these, an orthogonal evolutionary algorithm with LA for complex multiobjective optimization problems with continuous variables is proposed. The experimental results show that in continuous states, the proposed algorithm is able to achieve accurate Pareto-optimal sets and wide Pareto-optimal fronts efficiently. Moreover, the comparison with the several existing well-known algorithms: nondominated sorting genetic algorithm II, decomposition-based multiobjective evolutionary algorithm, decomposition-based multiobjective evolutionary algorithm with an ensemble of neighborhood sizes, multiobjective optimization by LA, and multiobjective immune algorithm with nondominated neighbor-based selection, on 15 multiobjective benchmark problems, shows that the proposed algorithm is able to find more accurate and evenly distributed Pareto-optimal fronts than the compared ones.

  3. Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases. (United States)

    Sagredo, Sandra; Pirzer, Tobias; Aghebat Rafat, Ali; Goetzfried, Marisa A; Moncalian, Gabriel; Simmel, Friedrich C; de la Cruz, Fernando


    DNA-binding proteins are promising reagents for the sequence-specific modification of DNA-based nanostructures. Here, we investigate the utility of a series of relaxase proteins-TrwC, TraI, and MobA-for nanofunctionalization. Relaxases are involved in the conjugative transfer of plasmids between bacteria, and bind to their DNA target sites via a covalent phosphotyrosine linkage. We study the binding of the relaxases to two standard DNA origami structures-rodlike six-helix bundles and flat rectangular origami sheets. We find highly orthogonal binding of the proteins with binding yields of 40-50 % per binding site, which is comparable to other functionalization methods. The yields differ for the two origami structures and also depend on the position of the binding sites. Due to their specificity for a single-stranded DNA target, their orthogonality, and their binding properties, relaxases are a uniquely useful addition to the toolbox available for the modification of DNA nanostructures with proteins. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  4. Efficient and Adaptive Orthogonal Finite Element Representation of the Geopotential (United States)

    Junkins, John L.; Younes, Ahmad Bani; Woollands, Robyn M.; Bai, Xiaoli


    We unify and extend classical results from function approximation theory and consider their utility in astrodynamics. Least square approximation, using the classical Chebyshev polynomials as basis functions, is reviewed for discrete samples of the to-be-approximated function. We extend the orthogonal approximation ideas to n-dimensions in a novel way, through the use of array algebra and Kronecker operations. Approximation of test functions illustrates the resulting algorithms and provides insight into the errors of approximation, as well as the associated errors arising when the approximations are differentiated or integrated. Two sets of applications are considered that are challenges in astrodynamics. The first application addresses local approximation of high degree and order geopotential models, replacing the global spherical harmonic series by a family of locally precise orthogonal polynomial approximations for efficient computation. A method is introduced which adapts the approximation degree radially, compatible with the truth that the highest degree approximations (to ensure maximum acceleration error < 10-9 m s-2, globally) are required near the Earth's surface, whereas lower degree approximations are required as radius increases. We show that a four order of magnitude speedup is feasible, with efficiency optimized using radial adaptation.

  5. Non-Orthogonal Multiple Access for Ubiquitous Wireless Sensor Networks. (United States)

    Anwar, Asim; Seet, Boon-Chong; Ding, Zhiguo


    Ubiquitous wireless sensor networks (UWSNs) have become a critical technology for enabling smart cities and other ubiquitous monitoring applications. Their deployment, however, can be seriously hampered by the spectrum available to the sheer number of sensors for communication. To support the communication needs of UWSNs without requiring more spectrum resources, the power-domain non-orthogonal multiple access (NOMA) technique originally proposed for 5th Generation (5G) cellular networks is investigated for UWSNs for the first time in this paper. However, unlike 5G networks that operate in the licensed spectrum, UWSNs mostly operate in unlicensed spectrum where sensors also experience cross-technology interferences from other devices sharing the same spectrum. In this paper, we model the interferences from various sources at the sensors using stochastic geometry framework. To evaluate the performance, we derive a theorem and present new closed form expression for the outage probability of the sensors in a downlink scenario under interference limited environment. In addition, diversity analysis for the ordered NOMA users is performed. Based on the derived outage probability, we evaluate the average link throughput and energy consumption efficiency of NOMA against conventional orthogonal multiple access (OMA) technique in UWSNs. Further, the required computational complexity for the NOMA users is presented.

  6. Bifurcations in two-image photometric stereo for orthogonal illuminations (United States)

    Kozera, R.; Prokopenya, A.; Noakes, L.; Śluzek, A.


    This paper discusses the ambiguous shape recovery in two-image photometric stereo for a Lambertian surface. The current uniqueness analysis refers to linearly independent light-source directions p = (0, 0, -1) and q arbitrary. For this case necessary and sufficient condition determining ambiguous reconstruction is governed by a second-order linear partial differential equation with constant coefficients. In contrast, a general position of both non-colinear illumination directions p and q leads to a highly non-linear PDE which raises a number of technical difficulties. As recently shown, the latter can also be handled for another family of orthogonal illuminations parallel to the OXZ-plane. For the special case of p = (0, 0, -1) a potential ambiguity stems also from the possible bifurcations of sub-local solutions glued together along a curve defined by an algebraic equation in terms of the data. This paper discusses the occurrence of similar bifurcations for such configurations of orthogonal light-source directions. The discussion to follow is supplemented with examples based on continuous reflectance map model and generated synthetic images.

  7. Cache-Oblivious Planar Orthogonal Range Searching and Counting

    DEFF Research Database (Denmark)

    Arge, Lars; Brodal, Gerth Stølting; Fagerberg, Rolf


    present the first cache-oblivious data structure for planar orthogonal range counting, and improve on previous results for cache-oblivious planar orthogonal range searching. Our range counting structure uses O(Nlog2 N) space and answers queries using O(logB N) memory transfers, where B is the block...... size of any memory level in a multilevel memory hierarchy. Using bit manipulation techniques, the space can be further reduced to O(N). The structure can also be modified to support more general semigroup range sum queries in O(logB N) memory transfers, using O(Nlog2 N) space for three-sided queries...... and O(Nlog22 N/log2log2 N) space for four-sided queries. Based on the O(Nlog N) space range counting structure, we develop a data structure that uses O(Nlog2 N) space and answers three-sided range queries in O(logB N+T/B) memory transfers, where T is the number of reported points. Based...

  8. The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G). (United States)

    Hirokawa, Go; Iwakura, Nobuhiro; Kaji, Akira; Kaji, Hideko


    Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splitting was observed with sucrose density gradient centrifugation (SDGC) without IF3 if RRF, EF-G and GTP were present in the SDGC buffer. The splitting of 70S ribosomes causes the decrease of light scattering by ribosomes. Kinetic constants obtained from the light scattering studies are sufficient to account for the splitting of 70S ribosomes by RRF and EF-G/GTP during the lag phase for activation of ribosomes for the log phase. As the amount of 70S ribosomes increased, more RRF, EF-G and GTP were necessary to split 70S ribosomes. In the presence of a physiological amount of polyamines, GTP and factors, even 0.6 microM 70S ribosomes (12 times higher than the 70S ribosomes for routine assay) were split. Spermidine (2 mM) completely inhibited anti-association activity of IF3, and the RRF/EF-G/GTP-dependent splitting of 70S ribosomes.

  9. CERN internal communication is evolving

    CERN Multimedia


    CERN news will now be regularly updated on the CERN People page (see here).      Dear readers, All over the world, communication is becoming increasingly instantaneous, with news published in real time on websites and social networks. In order to keep pace with these changes, CERN's internal communication is evolving too. From now on, you will be informed of what’s happening at CERN more often via the “CERN people” page, which will frequently be updated with news. The Bulletin is following this trend too: twice a month, we will compile the most important articles published on the CERN site, with a brand-new layout. You will receive an e-mail every two weeks as soon as this new form of the Bulletin is available. If you have interesting news or stories to share, tell us about them through the form at:​. You can also find out about news from CERN in real time...

  10. Rrp15p, a novel component of pre-ribosomal particles required for 60S ribosome subunit maturation (United States)



    In eukaryotes ribosome biogenesis required that rRNAs primary transcripts are assembled in pre-ribosomal particles and processed. Protein factors and pre-ribosomal complexes involved in this complex pathway are not completely depicted. The essential ORF YPR143W encodes in yeast for an uncharacterized protein product, named here Rrp15p. Cellular function of Rrp15p has not so far defined even if nucleolar location was referred. With the aim to define the possible role of this orphan gene, we performed TAP-tagging of Rrp15p and investigated its molecular association with known pre-ribosomal complexes. Comparative sucrose gradient sedimentation analyses of yeast lysates expressing the TAP-tagged Rrp15p, strongly indicated that this protein is a component of the pre-60S particles. Northern hybridization, primer extension and functional proteomics on TAP-affinity isolated complexes proved that Rrp15p predominately associated with pre-rRNAs and proteins previously characterized as components of early pre-60S ribosomal particles. Finally, depletion of Rrp15p inhibited the accumulation of 27S and 7S pre-rRNAs and 5.8S and 25S mature rRNA. These results provide the first indication that Rrp15p is a novel factor involved in the early maturation steps of the 60S subunits. Moreover, the identification of the protein kinase CK2 in the Rrp15p-containing pre-ribosomal particles here reported, sustains the link between ribosome synthesis and cell cycle progression. PMID:15769876

  11. Transcriptome-wide measurement of translation by ribosome profiling. (United States)

    McGlincy, Nicholas J; Ingolia, Nicholas T


    Translation is one of the fundamental processes of life. It comprises the assembly of polypeptides whose amino acid sequence corresponds to the codon sequence of an mRNA's ORF. Translation is performed by the ribosome; therefore, in order to understand translation and its regulation we must be able to determine the numbers and locations of ribosomes on mRNAs in vivo. Furthermore, we must be able to examine their redistribution in different physiological contexts and in response to experimental manipulations. The ribosome profiling method provides us with an opportunity to learn these locations, by sequencing a cDNA library derived from the short fragments of mRNA covered by the ribosome. Since its original description, the ribosome profiling method has undergone continuing development; in this article we describe the method's current state. Important improvements include: the incorporation of sample barcodes to enable library multiplexing, the incorporation of unique molecular identifiers to enable to removal of duplicated sequences, and the replacement of a gel-purification step with the enzymatic degradation of unligated linker. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Epigenetic engineering of ribosomal RNA genes enhances protein production.

    Directory of Open Access Journals (Sweden)

    Raffaella Santoro

    Full Text Available Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA genes encode the major component of the ribosome but many rRNA gene copies are not transcribed due to epigenetic silencing by the nucleolar remodelling complex (NoRC [6], which may limit the cell's full production capacity. Here we show that the knockdown of TIP5, a subunit of NoRC, decreases the number of silent rRNA genes, upregulates rRNA transcription, enhances ribosome synthesis and increases production of recombinant proteins. However, general enhancement of rRNA transcription rate did not stimulate protein synthesis. Our data demonstrates that the number of transcriptionally competent rRNA genes limits efficient ribosome synthesis. Epigenetic engineering of ribosomal RNA genes offers new possibilities for improving biopharmaceutical manufacturing and provides novel insights into the complex regulatory network which governs the translation machinery in normal cellular processes as well as in pathological conditions like cancer.

  13. A high-order q-difference equation for q-Hahn multiple orthogonal polynomials

    DEFF Research Database (Denmark)

    Arvesú, J.; Esposito, Chiara


    A high-order linear q-difference equation with polynomial coefficients having q-Hahn multiple orthogonal polynomials as eigenfunctions is given. The order of the equation coincides with the number of orthogonality conditions that these polynomials satisfy. Some limiting situations when are studie....... Indeed, the difference equation for Hahn multiple orthogonal polynomials given in Lee [J. Approx. Theory (2007), ), doi: 10.1016/j.jat.2007.06.002] is obtained as a limiting case....

  14. Passive Wireless Hydrogen Sensors Using Orthogonal Frequency Coded Acoustic Wave Devices Project (United States)

    National Aeronautics and Space Administration — This proposal describes the continued development of passive orthogonal frequency coded (OFC) surface acoustic wave (SAW) based hydrogen sensors for NASA application...

  15. Self-orthogonal codes with dual distance three and quantum codes with distance three over (United States)

    Liang, Fangchi


    Self-orthogonal codes with dual distance three and quantum codes with distance three constructed from self-orthogonal codes over are discussed in this paper. Firstly, for given code length , a self-orthogonal code with minimal dimension and dual distance three is constructed. Secondly, for each , two nested self-orthogonal codes with dual distance two and three are constructed, and consequently quantum code of length and distance three is constructed via Steane construction. All of these quantum codes constructed via Steane construction are optimal or near optimal according to the quantum Hamming bound.

  16. Orthogonal spline collocation methods for partial differential equations (United States)

    Bialecki, B.; Fairweather, G.


    This paper provides an overview of the formulation, analysis and implementation of orthogonal spline collocation (OSC), also known as spline collocation at Gauss points, for the numerical solution of partial differential equations in two space variables. Advances in the OSC theory for elliptic boundary value problems are discussed, and direct and iterative methods for the solution of the OSC equations examined. The use of OSC methods in the solution of initial-boundary value problems for parabolic, hyperbolic and Schrödinger-type systems is described, with emphasis on alternating direction implicit methods. The OSC solution of parabolic and hyperbolic partial integro-differential equations is also mentioned. Finally, recent applications of a second spline collocation method, modified spline collocation, are outlined.

  17. Orthogonal-coil RF probe for implantable passive sensors. (United States)

    Talman, James R; Fleischman, Aaron J; Roy, Shuvo


    A versatile orthogonal-coil radio frequency (RF) probe suitable for detecting the resonant frequency of miniature implantable passive sensors has been designed and tested. The probe sensitivity has been tested using printed-circuit spiral inductors of various sizes (3-15 mm) in series with discrete surface-mount capacitors designed to resonate over a range of frequencies (50-200 MHz). Close agreement between theoretical calculations and experimental results has been obtained. An equation is derived for transmit/receive (T/R) isolation that agrees with experimental measurements over the frequency range 1-500 MHz. The probe includes an additional coil to compensate for the effect of eddy currents in the human body on the probe. T/R isolation of at least 90 dB over the frequency range 1-100 MHz can be achieved when the probe is placed in close proximity to the human body.

  18. Effects of orthogonal rotating electric fields on electrospinning process (United States)

    Lauricella, M.; Cipolletta, F.; Pontrelli, G.; Pisignano, D.; Succi, S.


    Electrospinning is a nanotechnology process whereby an external electric field is used to accelerate and stretch a charged polymer jet, so as to produce fibers with nanoscale diameters. In quest of a further reduction in the cross section of electrified jets hence of a better control on the morphology of the resulting electrospun fibers, we explore the effects of an external rotating electric field orthogonal to the jet direction. Through intensive particle simulations, it is shown that by a proper tuning of the electric field amplitude and frequency, a reduction of up to a 30% in the aforementioned radius can be obtained, thereby opening new perspectives in the design of future ultra-thin electrospun fibers. Applications can be envisaged in the fields of nanophotonic components as well as for designing new and improved filtration materials.

  19. Combining minutiae triplets and quaternion orthogonal moments for fingerprint verification (United States)

    Haloui, Lamyae; En-Nahnahi, Noureddine; Ouatik, Said El Alaoui


    We introduce a hybrid fingerprint recognition method built from minutiae and quaternion orthogonal moments. The proposed algorithm includes four steps: extraction of the minutiae triplets (m-triplets), first pass of triplets minutiae matching, validation step of these triplets by characterizing their neighboring gray-level image information through feature vectors of quaternion radial moments, and an adequate similarity measure. By boosting the local minutiae matching step, we avoid consolidation and global matching. To show the added-value of our method, several algorithms for extracting and matching m-triplets are considered and an experimental comparison is established. Experiments are carried out using all four parts of the FVC2004 dataset. Results indicate that the combination of the geometrical features and the quaternion radial moments of the m-triplets leads to an improvement in the overall fingerprint matching performance and demonstrate the expected gain of integrating a validation step in an m-triplets based fingerprint matching algorithm.

  20. Downlink scheduling using non-orthogonal uplink beams

    KAUST Repository

    Eltayeb, Mohammed E.


    Opportunistic schedulers rely on the feedback of the channel state information of users in order to perform user selection and downlink scheduling. This feedback increases with the number of users, and can lead to inefficient use of network resources and scheduling delays. We tackle the problem of feedback design, and propose a novel class of nonorthogonal codes to feed back channel state information. Users with favorable channel conditions simultaneously transmit their channel state information via non-orthogonal beams to the base station. The proposed formulation allows the base station to identify the strong users via a simple correlation process. After deriving the minimum required code length and closed-form expressions for the feedback load and downlink capacity, we show that i) the proposed algorithm reduces the feedback load while matching the achievable rate of full feedback algorithms operating over a noiseless feedback channel, and ii) the proposed codes are superior to the Gaussian codes.

  1. Optimizing Orthogonal Multiple Access based on Quantized Channel State Information

    CERN Document Server

    Marques, Antonio G; Ramos, Javier


    The performance of systems where multiple users communicate over wireless fading links benefits from channel-adaptive allocation of the available resources. Different from most existing approaches that allocate resources based on perfect channel state information, this work optimizes channel scheduling along with per user rate and power loadings over orthogonal fading channels, when both terminals and scheduler rely on quantized channel state information. Channel-adaptive policies are designed to optimize an average transmit-performance criterion subject to average quality of service requirements. While the resultant optimal policy per fading realization shows that the individual rate and power loadings can be obtained separately for each user, the optimal scheduling is slightly more complicated. Specifically, per fading realization each channel is allocated either to a single (winner) user, or, to a small group of winner users whose percentage of shared resources is found by solving a linear program. A singl...

  2. Total energy global optimizations using non orthogonal localized orbitals

    CERN Document Server

    Kim, J; Galli, G; Kim, Jeongnim; Mauri, Francesco; Galli, Giulia


    An energy functional for orbital based $O(N)$ calculations is proposed, which depends on a number of non orthogonal, localized orbitals larger than the number of occupied states in the system, and on a parameter, the electronic chemical potential, determining the number of electrons. We show that the minimization of the functional with respect to overlapping localized orbitals can be performed so as to attain directly the ground state energy, without being trapped at local minima. The present approach overcomes the multiple minima problem present within the original formulation of orbital based $O(N)$ methods; it therefore makes it possible to perform $O(N)$ calculations for an arbitrary system, without including any information about the system bonding properties in the construction of the input wavefunctions. Furthermore, while retaining the same computational cost as the original approach, our formulation allows one to improve the variational estimate of the ground state energy, and the energy conservation...

  3. The performance of proper orthogonal decomposition in discontinuous flows

    Directory of Open Access Journals (Sweden)

    Jing Li


    Full Text Available In this paper, flow reconstruction accuracy and flow prediction capability of discontinuous transonic flow field by means of proper orthogonal decomposition (POD method is studied. Although linear superposition of “high frequency waves” in different POD modes can achieve the reconstruction of the shock wave, the smoothness of the solution near the shock wave cannot be guaranteed. The modal coefficients are interpolated or extrapolated and different modal components are superposed to realize the prediction of the flow field beyond the snapshot sets. Results show that compared with the subsonic flow, the transonic flow with shock wave requires more POD modes to reach a comparative reconstruction accuracy. When a shock wave exists, the interpolation prediction ability is acceptable. However, large errors exist in extrapolation, and increasing the number of POD modes cannot effectively improve the prediction accuracy of the flow field.

  4. Orthogonal Bases used for Feed Forward Control of Wind Turbines

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh; Stoustrup, Jakob


    In optimizing wind turbines it can be of a large help to use information of wind speeds at upwind turbine for the control of downwind turbines, it is, however, problematic to use these measurements directly since they are highly influenced by turbulence behind the wind turbine rotor plane. In this......In optimizing wind turbines it can be of a large help to use information of wind speeds at upwind turbine for the control of downwind turbines, it is, however, problematic to use these measurements directly since they are highly influenced by turbulence behind the wind turbine rotor plane....... In this paper an orthogonal basis is use to extract the general trends in the wind signal, which are forward to the down wind turbines. This concept controller is designed and simulated on a generic 4.8 MW wind turbine model, which shows the potential of this proposed scheme....

  5. Interaction of tRNA with Eukaryotic Ribosome

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer


    Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.

  6. Structural basis for precursor protein-directed ribosomal peptide macrocyclization

    Energy Technology Data Exchange (ETDEWEB)

    Li, Kunhua; Condurso, Heather L.; Li, Gengnan; Ding, Yousong; Bruner, Steven D. (Florida)


    Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein–protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.

  7. 5SRNAdb: an information resource for 5S ribosomal RNAs. (United States)

    Szymanski, Maciej; Zielezinski, Andrzej; Barciszewski, Jan; Erdmann, Volker A; Karlowski, Wojciech M


    Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb ( is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Ribosomal Chamber Music: Toward an Understanding of IRES Mechanisms. (United States)

    Yamamoto, Hiroshi; Unbehaun, Anett; Spahn, Christian M T


    Internal initiation is a 5'-end-independent mode of translation initiation engaged by many virus- and putatively some cell-encoded templates. Internal initiation is facilitated by specific RNA tertiary folds, called internal ribosomal entry sites (IRESs), in the 5' untranslated region (UTR) of the respective transcripts. In this review we discuss recent structural insight into how established IRESs first capture and then manipulate the eukaryotic translation machinery through non-canonical interactions and by guiding the intrinsic conformational flexibility of the eukaryotic ribosome. Because IRESs operate with reduced complexity and constitute minimal systems of initiation, comparison with canonical initiation may allow common mechanistic principles of the ribosome to be delineated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. (United States)

    Kornprobst, Markus; Turk, Martin; Kellner, Nikola; Cheng, Jingdong; Flemming, Dirk; Koš-Braun, Isabelle; Koš, Martin; Thoms, Matthias; Berninghausen, Otto; Beckmann, Roland; Hurt, Ed


    The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Orthogonal relations and color constancy in dichromatic colorblindness.

    Directory of Open Access Journals (Sweden)

    Ralph W Pridmore

    Full Text Available This paper employs uniform color space to analyze relations in dichromacy (protanopia, deuteranopia, tritanopia. Fifty percent or less of dichromats represent the classical reduction form of trichromacy, where one of three cones is inoperative but normal trichromatic color mixture such as complementary colors (pairs that mix white are accepted by the dichromat, whose data can thus be plotted to CIE chromaticity spaces. The remaining dichromats comprise many and varied more-complex gene arrays from mutations, recombinations, etc. Though perhaps a minority, the three reductionist types provide a simple standard, in genotype and phenotype, to which the more complex remainder may be compared. Here, previously published data on dichromacy are plotted and analyzed in CIELUV uniform color space to find spatial relations in terms of color appearance space (e.g., hue angle. Traditional residual (seen hues for protanopia and deuteranopia (both red-green colorblindness are yellow and blue, but analysis indicates the protanopic residual hues are more greenish yellow and reddish blue than in tradition. Results for three illuminants (D65, D50, B imply four principles in the spatial structure of dichromacy: (1 complementarity of confusion hue pairs and of residual hue pairs; (2 orthogonality of confusion locus and residual hues locus at their intersection with the white point, in each dichromatic type; (3 orthogonality of protanopic and tritanopic confusion loci; and (4 inverse relations between protanopic and tritanopic systems generally, such that one's confusion hues are the other's residual hues. Two of the three dichromatic systems do not represent components of normal trichromatic vision as sometimes thought but are quite different. Wavelength shifts between illuminants demonstrate chromatic adaptation correlates exactly with that in trichromatic vision. In theory these results clarify relations in and between types of dichromacy. They also apply in

  11. Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research. (United States)

    Schäkermann, Sina; Prochnow, Pascal; Bandow, Julia E


    Current research is focusing on ribosome heterogeneity as a response to changing environmental conditions and stresses, such as antibiotic stress. Altered stoichiometry and composition of ribosomal proteins as well as association of additional protein factors are mechanisms for shaping the protein expression profile or hibernating ribosomes. Here, we present a method for the isolation of ribosomes to analyze antibiotic-induced changes in the composition of ribosomes in Bacillus subtilis or other bacteria. Ribosomes and associated proteins are isolated by ultracentrifugation and proteins are identified and quantified using label-free mass spectrometry.

  12. Protein-protein interactions within late pre-40S ribosomes.

    Directory of Open Access Journals (Sweden)

    Melody G Campbell


    Full Text Available Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.

  13. Architecture of the E.coli 70S ribosome

    DEFF Research Database (Denmark)

    Burkhardt, N.; Diedrich, G.; Nierhaus, K.H.


    The 70S ribosome from E.coli was analysed by neutron scattering focusing on the shape and the internal protein-RNA-distribution of the complex. Measurements on selectively deuterated 70S particles and free 30S and 50S subunits applying conventional contrast variation and proton-spin contrast......-variation resulted in a total of 42 scattering curves. Processing the data on the basis of the spherical harmonic technique, a four-phase model for the 70S ribosome could be generated, which describes the shape of the particle as well as the protein- and the RNA-moieties of each subunit at about 35 Angstrom...

  14. Ribosomal crystallography: from crystal growth to initial phasing (United States)

    Thygesen, J.; Krumbholz, S.; Levin, I.; Zaytzev-Bashan, A.; Harms, J.; Bartels, H.; Schlünzen, F.; Hansen, H. A. S.; Bennett, W. S.; Volkmann, N.; Agmon, I.; Eisenstein, M.; Dribin, A.; Maltz, E.; Sagi, I.; Morlang, S.; Fua, M.; Franceschi, F.; Weinstein, S.; Böddeker, N.; Sharon, R.; Anagnostopoulos, K.; Peretz, M.; Geva, M.; Berkovitch-Yellin, Z.; Yonath, A.


    Preliminary phases were determined by the application of the isomorphous replacement method at low and intermediate resolution for structure factor amplitudes collected from crystals of large and small ribosomal subunits from halophilic and thermophilic bacteria. Derivatization was performed with dense heavy atom clusters, either by soaking or by specific covalent binding prior to the crystallization. The resulting initial electron density maps contain features comparable in size to those expected for the corresponding particles. The packing arrangements of these maps have been compared with motifs observed by electron microscopy in positively stained thin sections of embedded three-dimensional crystals, as well as with phase sets obtained by ab-initio computations. Aimed at higher resolution phasing, procedures are being developed for multi-site binding of relatively small dense metal clusters at selected locations. Potential sites are being inserted either by mutagenesis or by chemical modifications to facilitate cluster binding to the large halophilic and the small thermophilic ribosomal subunits which yield crystals diffracting to the highest resolution obtained so far for ribosomes, 2.9 and 7.3 Å, respectively. For this purpose the surfaces of these ribosomal particles have been characterized and conditions for quantitative reversible detachment of selected ribosomal proteins have been found. The corresponding genes are being cloned, sequenced, mutated to introduce the reactive side-groups (mainly cysteines) and overexpressed. To assist the interpretation of the anticipated electron density maps, sub-ribosomal stable complexes were isolated from H50S. One of these complexes is composed of two proteins and the other is made of a stretch of the rRNA and a protein. For exploiting the exposed parts of the surface of these complexes for heavy atom binding and for attempting the determination of their three-dimensional structure, their components are being produced

  15. Combined Effect of the Cfr Methyltransferase and Ribosomal Protein L3 Mutations on Resistance to Ribosome-Targeting Antibiotics

    DEFF Research Database (Denmark)

    Pakula, Kevin K; Hansen, Lykke H; Vester, Birte


    Several groups of antibiotics inhibit bacterial growth by binding to bacterial ribosomes. Mutations in ribosomal protein L3 have been associated with resistance to linezolid and tiamulin, which both bind at the peptidyl transferase center in the ribosome. Resistance to these and other antibiotics...... also occurs through methylation of 23S rRNA at position A2503 by the methyltransferase Cfr. The mutations in L3 and the cfr gene have been found together in clinical isolates, raising the question of whether they have a combined effect on antibiotic resistance or growth. We transformed a plasmid...... seen. This study underscores the complex interplay between various resistance mechanisms and cross-resistance, even from antibiotics with overlapping binding sites....

  16. COXPD9 an Evolving Multisystem Disease; Congenital Lactic Acidosis, Sensorineural Hearing Loss, Hypertrophic Cardiomyopathy, Cirrhosis and Interstitial Nephritis. (United States)

    Bursle, C; Narendra, A; Chuk, R; Cardinal, J; Justo, R; Lewis, B; Coman, D


    We present the second report of combined oxidative phosphorylation deficiency-9. The infant presented in the neonatal period with poor feeding, lactic acidosis and sensorineural hearing loss. He subsequently developed a lethal hypertrophic cardiomyopathy during infancy. Cirrhosis and interstitial nephritis were identified at autopsy. Exome sequencing has detected compound heterozygous mutations in the MRPL3 gene which encodes a large mitochondrial ribosome subunit protein. We identified a known heterozygous variant NM_007208 c.950>G (Pro317Arg) in the MRPL3 gene and a novel heterozygous mutation NM_007208 c.49delC p.(Arg17Aspfs*57). Mutations in MRPL3 have previously been shown to alter ribosome assembly and cause abnormal function of multiple respiratory chain complexes. Our case adds to the evolving knowledge of disorders of mitochondrial translation.

  17. DNA evolved to minimize frameshift mutations


    Agoni, Valentina


    Point mutations can surely be dangerous but what is worst than to lose the reading frame?! Does DNA evolved a strategy to try to limit frameshift mutations?! Here we investigate if DNA sequences effectively evolved a system to minimize frameshift mutations analyzing the transcripts of proteins with high molecular weights.

  18. Interaction between Bacillus subtilis YsxC and ribosomes (or rRNAs). (United States)

    Wicker-Planquart, Catherine; Jault, Jean-Michel


    YsxC is an essential P-loop GTPase, that binds to the 50S ribosomal subunit, and is required for the proper assembly of the ribosome. The aim of this study was to characterize YsxC ribosome interactions. The stoichiometry of YsxC ribosome subunit complex was evaluated. We showed that YsxC binding to the 50S ribosomal subunit is not affected by GTP, but in the presence of GDP the stoichiometry of YsxC-ribosome is decreased. YsxC GTPase activity was stimulated upon 50S ribosomal subunit binding. In addition, it is shown for the first time that YsxC binds both 16S and 23S ribosomal RNAs. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  19. Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. (United States)

    Greber, Basil J; Boehringer, Daniel; Godinic-Mikulcic, Vlatka; Crnkovic, Ana; Ibba, Michael; Weygand-Durasevic, Ivana; Ban, Nenad


    Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Novel Orthogonal Signal Based Decomposition of Digital Signals: Application to Sensor Fusion

    Directory of Open Access Journals (Sweden)

    Abdul Faheem Mohed


    Full Text Available In this research paper, a novel orthogonal decomposition of an arbitrary “digital” signal is proposed. An approach to attack the problem of wireless sensor fusion using digital signal processing techniques is discussed. The merits of the proposed orthogonal decomposition are briefly discussed. Simulation results are presented to illustrate the effectiveness of the proposed method.

  1. The band method and inverse problems for orthogonal matrix functions of Szego-Krein type

    NARCIS (Netherlands)

    Kaashoek, M.A.; Lerer, L.


    A band method approach for solving inverse problems for certain orthogonal functions is developed. The inverse theorems for Szego-Kreǐn matrix polynomials and for Kreǐn orthogonal entire matrix functions are obtained as corollaries of the band method results. Other examples, including a

  2. Application of orthogonal light scattering for routine screening of lymphocyte samples

    NARCIS (Netherlands)

    Terstappen, Leonardus Wendelinus Mathias Marie; de Grooth, B.G.; van Berkel, W.; ten Napel, C.H.H.; Greve, Jan


    Orthogonal and forward light-scattering properties of lymphocytes were measured from patients with different lymphocytic diseases in order to determine the potential value of light scattering as a screening device. Monitoring of orthogonal light scattering of lymphocytes of a B-cell chronic

  3. Aspects of Orthogonality in the Development of the National Digital Wealth (NDW

    Directory of Open Access Journals (Sweden)

    Ion IVAN


    Full Text Available There are presented aspects of orthogonality in the development of the national digital wealth. There is presented the concept of NDW. Are identified quality characteristics. Are built orthogonality metrics for software development applications which are parts of NDW.

  4. Generalized Christoffel-Darboux formula for skew-orthogonal polynomials and random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Saugata [Abdus Salam ICTP, Strada Costiera 11, 34100, Trieste (Italy)


    We obtain a generalized Christoffel-Darboux (GCD) formula for skew-orthogonal polynomials. Using this, we present an alternative derivation of the level density and two-point function for Gaussian orthogonal ensembles and Gaussian symplectic ensembles of random matrices.

  5. Non-orthogonal version of the arbitrary polygonal C-grid and a new diamond grid

    Directory of Open Access Journals (Sweden)

    H. Weller


    Full Text Available Quasi-uniform grids of the sphere have become popular recently since they avoid parallel scaling bottlenecks associated with the poles of latitude–longitude grids. However quasi-uniform grids of the sphere are often non-orthogonal. A version of the C-grid for arbitrary non-orthogonal grids is presented which gives some of the mimetic properties of the orthogonal C-grid. Exact energy conservation is sacrificed for improved accuracy and the resulting scheme numerically conserves energy and potential enstrophy well. The non-orthogonal nature means that the scheme can be used on a cubed sphere. The advantage of the cubed sphere is that it does not admit the computational modes of the hexagonal or triangular C-grids. On various shallow-water test cases, the non-orthogonal scheme on a cubed sphere has accuracy less than or equal to the orthogonal scheme on an orthogonal hexagonal icosahedron. A new diamond grid is presented consisting of quasi-uniform quadrilaterals which is more nearly orthogonal than the equal-angle cubed sphere but with otherwise similar properties. It performs better than the cubed sphere in every way and should be used instead in codes which allow a flexible grid structure.

  6. A note on the zeros of Freud-Sobolev orthogonal polynomials (United States)

    Moreno-Balcazar, Juan J.


    We prove that the zeros of a certain family of Sobolev orthogonal polynomials involving the Freud weight function e-x4 on are real, simple, and interlace with the zeros of the Freud polynomials, i.e., those polynomials orthogonal with respect to the weight function e-x4. Some numerical examples are shown.

  7. The characterization of cytoplasmic ribosomal protein genes in ...

    African Journals Online (AJOL)



    Apr 17, 2012 ... genomics' characteristics, a genome-wide survey in N. bombycis genome was performed. From the results, we ... bombycis ESTs, and they have the same structure among microsporidia. The novel arrangements of ...... chromosome and ribosomal DNA organization in the context of the complete genome ...

  8. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering (United States)

    Zaccai, Giuseppe; Natali, Francesca; Peters, Judith; Řihová, Martina; Zimmerman, Ella; Ollivier, J.; Combet, J.; Maurel, Marie-Christine; Bashan, Anat; Yonath, Ada


    Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.

  9. cDNA, genomic sequence cloning and overexpression of ribosomal ...

    African Journals Online (AJOL)

    RPS16 of eukaryote is a component of the 40S small ribosomal subunit encoded by RPS16 gene and is also a homolog of prokaryotic RPS9. The cDNA and genomic sequence of RPS16 was cloned successfully for the first time from the Giant Panda (Ailuropoda melanoleuca) using reverse transcription-polymerase chain ...

  10. cDNA, genomic sequence cloning and overexpression of ribosomal ...

    African Journals Online (AJOL)



    Nov 2, 2009 ... RPS20 is a component of the 40S small ribosomal subunit encoded by RPS20 gene, which is conserved between eukaryotes, prokaryotes and archaebacteria. The cDNA and the genomic sequence of RPS20 were cloned successfully from the Giant Panda (Ailuropoda melanoleuca) using RT-PCR ...

  11. The putative E. histolytica orthologue of the human ribosomal RNA ...

    Indian Academy of Sciences (India)


    Feb 4, 2016 ... similarity (Altschul et al. 1997). The transcription, processing, and assembly of pre- ribosomal particles takes place in the nucleolus (Venema and Tollervey 1999). Ultrastructural studies on. E. histolytica nucleus by electron microscopy showed that chromatin, apart from being diffusely distributed in the nu-.

  12. The ribosome-associated complex antagonizes prion formation in yeast. (United States)

    Amor, Alvaro J; Castanzo, Dominic T; Delany, Sean P; Selechnik, Daniel M; van Ooy, Alex; Cameron, Dale M


    The number of known fungal proteins capable of switching between alternative stable conformations is steadily increasing, suggesting that a prion-like mechanism may be broadly utilized as a means to propagate altered cellular states. To gain insight into the mechanisms by which cells regulate prion formation and toxicity we examined the role of the yeast ribosome-associated complex (RAC) in modulating both the formation of the [PSI(+)] prion - an alternative conformer of Sup35 protein - and the toxicity of aggregation-prone polypeptides. The Hsp40 RAC chaperone Zuo1 anchors the RAC to ribosomes and stimulates the ATPase activity of the Hsp70 chaperone Ssb. We found that cells lacking Zuo1 are sensitive to over-expression of some aggregation-prone proteins, including the Sup35 prion domain, suggesting that co-translational protein misfolding increases in Δzuo1 strains. Consistent with this finding, Δzuo1 cells exhibit higher frequencies of spontaneous and induced prion formation. Cells expressing mutant forms of Zuo1 lacking either a C-terminal charged region required for ribosome association, or the J-domain responsible for Ssb ATPase stimulation, exhibit similarly high frequencies of prion formation. Our findings are consistent with a role for the RAC in chaperoning nascent Sup35 to regulate folding of the N-terminal prion domain as it emerges from the ribosome.

  13. Ribosomal DNA internal transcribed spacer 1 and internal ...

    African Journals Online (AJOL)



    Jul 26, 2010 ... in some East Asian countries such as China, Korea and. *Corresponding author. E-mail: Tel: +82 33 250 6476. Fax: +82 33 250 6470. Abbreviations: nrDNA, Nuclear ribosomal DNA; ITS, internal transcribed spacer; PCR, polymerase chain reaction; BLAST, basic local alignment ...

  14. Expression of a ribosome inactivating protein (curcin 2) in Jatropha ...

    Indian Academy of Sciences (India)

    Expression of a ribosome inactivating protein (curcin 2) in Jatropha curcas is induced by stress ... In addition, the 32 kDa band is nearly the molecular weight of curcin 2. ... curcin 2. The presence of this protein molecular marker under stresses may provide an experimental foundation to study the stress proteins in J. curcas.

  15. Cloning and expression of antiviral/ribosome-inactivating protein ...

    Indian Academy of Sciences (India)


    Feb 2, 2008 ... The ORF was cloned into an expression vector and expressed in E. coli as a fusion protein of ∼78 kDa. The cleaved and purified recombinant BBAP1 exhibited ribosome-inhibiting rRNA -glycosidase activity, and imparted a high level of resistance against the tobacco mosaic virus (TMV).

  16. PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Ryuji J Machida

    Full Text Available BACKGROUND: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. METHODOLOGY/PRINCIPAL FINDINGS: A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. CONCLUSIONS/SIGNIFICANCE: Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.

  17. The HIV Tat protein affects processing of ribosomal RNA precursor

    Directory of Open Access Journals (Sweden)

    Bellenchi Gian


    Full Text Available Abstract Background Inside the cell, the HIV Tat protein is mainly found in the nucleus and nucleolus. The nucleolus, the site of ribosome biogenesis, is a highly organized, non-membrane-bound sub-compartment where proteins with a high affinity for nucleolar components are found. While it is well known that Tat accumulates in the nucleolus via a specific nucleolar targeting sequence, its function in this compartment it still unknown. Results To clarify the significance of the Tat nucleolar localization, we induced the expression of the protein during oogenesis in Drosophila melanogaster strain transgenic for HIV-tat gene. Here we show that Tat localizes in the nucleoli of Drosophila oocyte nurse cells, where it specifically co-localizes with fibrillarin. Tat expression is accompanied by a significant decrease of cytoplasmic ribosomes, which is apparently related to an impairment of ribosomal rRNA precursor processing. Such an event is accounted for by the interaction of Tat with fibrillarin and U3 snoRNA, which are both required for pre-rRNA maturation. Conclusion Our data contribute to understanding the function of Tat in the nucleolus, where ribosomal RNA synthesis and cell cycle control take place. The impairment of nucleolar pre-rRNA maturation through the interaction of Tat with fibrillarin-U3snoRNA complex suggests a process by which the virus modulates host response, thus contributing to apoptosis and protein shut-off in HIV-uninfected cells.

  18. Mechanism of recycling of post-termination ribosomal complexes in ...

    Indian Academy of Sciences (India)


    participate in this crucial process to free the ribosomal subunits for a new round of translation. We discuss the over- all pathway of ... uled translation reinitiation downstream of the stop codon. (Janosi et al 1998). RRF has also ..... Clearly, such knowledge would be important in exploiting. RRF as a target for newer drugs.

  19. Nuclear ribosomal DNA diversity of a cotton pest ( Rotylenchulus ...

    African Journals Online (AJOL)

    The reniform nematode (Rotylenchulus reniformis) has emerged as a major cotton pest in the United States. A recent analysis of over 20 amphimictic populations of this pest from the US and three other countries has shown no sequence variation at the nuclear ribosomal internal transcribed spacer (ITS) despite the region's ...

  20. mRNA pseudoknot structures can act as ribosomal roadblocks

    DEFF Research Database (Denmark)

    Hansen, Jesper Tholstrup; Oddershede, Lene Broeng; Sørensen, Michael Askvad


    Several viruses utilize programmed ribosomal frameshifting mediated by mRNA pseudoknots in combination with a slippery sequence to produce a well defined stochiometric ratio of the upstream encoded to the downstream-encoded protein. A correlation between the mechanical strength of mRNA pseudoknots...

  1. A streamlined ribosome profiling protocol for the characterization of microorganisms

    DEFF Research Database (Denmark)

    Latif, Haythem; Szubin, Richard; Tan, Justin


    Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used...... fraction of informative reads, all while retaining the high quality standards of the existing protocol....

  2. Mechanism of recycling of post-termination ribosomal complexes in ...

    Indian Academy of Sciences (India)

    We discuss the overall pathway of ribosome recycling in eubacteria with especial reference to the important role of the initiation factor 3 (IF3) in this process. Depending on the step(s) at which IF3 function is implicated, three models have been proposed. In model 1, RRF and EFG dissociate the post-TCs into the 50S and ...

  3. Structure based hypothesis of a mitochondrial ribosome rescue mechanism

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A


    Full Text Available Abstract Background mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions that are conserved among mtRF1 sequences but that are different in their mtRF1a paralogs. We subsequently modeled the 3D structure of mtRF1a and mtRF1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtRF1. Results Our model predicts, in agreement with the experimental data, that the 3D structure of mtRF1a allows it to recognize the stop codons UAA and UAG in the A-site of the ribosome. In contrast, we show that mtRF1 likely can only bind the ribosome when the A-site is devoid of mRNA. Furthermore, while mtRF1a will adopt its catalytic conformation, in which it functions as a peptidyl-tRNA hydrolase in the ribosome, only upon binding of a stop codon in the A-site, mtRF1 appears specifically adapted to assume this extended, peptidyl-tRNA hydrolyzing conformation in the absence of mRNA in the A-site. Conclusions We predict that mtRF1 specifically recognizes ribosomes with an empty A-site and is able to function as a peptidyl-tRNA hydrolase in those situations. Stalled ribosomes with empty A-sites that still contain a tRNA bound to a peptide chain can result from the translation of truncated, stop-codon less mRNAs. We hypothesize that mtRF1 recycles such stalled ribosomes, performing a function that is analogous to that of tmRNA in bacteria. Reviewers This article was reviewed by Dr. Eugene Koonin, Prof. Knud H. Nierhaus (nominated by Dr. Sarah Teichmann and Dr. Shamil Sunyaev.

  4. Orthogonal analysis of functional gold nanoparticles for biomedical applications. (United States)

    Tsai, De-Hao; Lu, Yi-Fu; DelRio, Frank W; Cho, Tae Joon; Guha, Suvajyoti; Zachariah, Michael R; Zhang, Fan; Allen, Andrew; Hackley, Vincent A


    We report a comprehensive strategy based on implementation of orthogonal measurement techniques to provide critical and verifiable material characteristics for functionalized gold nanoparticles (AuNPs) used in biomedical applications. Samples were analyzed before and after ≈50 months of cold storage (≈4 °C). Biomedical applications require long-term storage at cold temperatures, which could have an impact on AuNP therapeutics. Thiolated polyethylene glycol (SH-PEG)-conjugated AuNPs with different terminal groups (methyl-, carboxylic-, and amine-) were chosen as a model system due to their high relevancy in biomedical applications. Electrospray-differential mobility analysis, asymmetric-flow field flow fractionation, transmission electron microscopy, scanning electron microscopy, atomic force microscopy, inductively coupled plasma mass spectrometry, and small-angle X-ray scattering were employed to provide both complementary and orthogonal information on (1) particle size and size distribution, (2) particle concentrations, (3) molecular conjugation properties (i.e., conformation and surface packing density), and (4) colloidal stability. Results show that SH-PEGs were conjugated on the surface of AuNPs to form a brush-like polymer corona. The surface packing density of SH-PEG was ≈0.42 nm(-2) for the methyl-PEG-SH AuNPs, ≈0.26 nm(-2) for the amine-SH-PEG AuNPs, and ≈0.18 nm(-2) for the carboxylic-PEG-SH AuNPs before cold storage, approximately 10 % of its theoretical maximum value. The conformation of surface-bound SH-PEGs was then estimated to be in an intermediate state between brush-like and random-coiled, based on the measured thicknesses in liquid and in dry states. By analyzing the change in particle size distribution and number concentration in suspension following cold storage, the long term colloidal stability of AuNPs was shown to be significantly improved via functionalization with SH-PEG, especially in the case of methyl-PEG-SH and carboxylic

  5. A novel method of constructing compactly supported orthogonal scaling functions from splines

    Directory of Open Access Journals (Sweden)

    Shouzhi Yang


    Full Text Available Abstract A novel construction of compactly supported orthogonal scaling functions and wavelets with spline functions is presented in this paper. Let M n $M_{n}$ be the center B-spline of order n, except for the case of order one, we know M n $M_{n}$ is not orthogonal. But by the formula of orthonormalization procedure, we can construct an orthogonal scaling function corresponding to M n $M_{n}$ . However, unlike M n $M_{n}$ itself, this scaling function no longer has compact support. To induce the orthogonality while keeping the compact support of M n $M_{n}$ , we put forward a simple, yet efficient construction method that uses the formula of orthonormalization procedure and the weighted average method to construct the two-scale symbol of some compactly supported orthogonal scaling functions.

  6. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. (United States)

    Calo, Eliezer; Flynn, Ryan A; Martin, Lance; Spitale, Robert C; Chang, Howard Y; Wysocka, Joanna


    DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.

  7. DNA replication stress restricts ribosomal DNA copy number. (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L


    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  8. DNA replication stress restricts ribosomal DNA copy number.

    Directory of Open Access Journals (Sweden)

    Devika Salim


    Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  9. Requirement of Neuronal Ribosome Synthesis for Growth and Maintenance of the Dendritic Tree* (United States)

    Slomnicki, Lukasz P.; Pietrzak, Maciej; Vashishta, Aruna; Jones, James; Lynch, Nicholas; Elliot, Shane; Poulos, Eric; Malicote, David; Morris, Bridgit E.; Hallgren, Justin; Hetman, Michal


    The nucleolus serves as a principal site of ribosome biogenesis but is also implicated in various non-ribosomal functions, including negative regulation of the pro-apoptotic transcription factor p53. Although disruption of the nucleolus may trigger the p53-dependent neuronal death, neurotoxic consequences of a selective impairment of ribosome production are unclear. Here, we report that in rat forebrain neuronal maturation is associated with a remarkable expansion of ribosomes despite postnatal down-regulation of ribosomal biogenesis. In cultured rat hippocampal neurons, inhibition of the latter process by knockdowns of ribosomal proteins S6, S14, or L4 reduced ribosome content without disrupting nucleolar integrity, cell survival, and signaling responses to the neurotrophin brain-derived neurotrophic factor. Moreover, reduced general protein synthesis and/or formation of RNA stress granules suggested diminished ribosome recruitment to at least some mRNAs. Such a translational insufficiency was accompanied by impairment of brain-derived neurotrophic factor-mediated dendritic growth. Finally, RNA stress granules and smaller dendritic trees were also observed when ribosomal proteins were depleted from neurons with established dendrites. Thus, a robust ribosomal apparatus is required to carry out protein synthesis that supports dendritic growth and maintenance. Consequently, deficits of ribosomal biogenesis may disturb neurodevelopment by reducing neuronal connectivity. Finally, as stress granule formation and dendritic loss occur early in neurodegenerative diseases, disrupted homeostasis of ribosomes may initiate and/or amplify neurodegeneration-associated disconnection of neuronal circuitries. PMID:26757818

  10. Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale (United States)

    Michel, Audrey M; Baranov, Pavel V


    Ribosome profiling or ribo-seq is a new technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome protected mRNA fragments allowing the measurement of ribosome density along all RNA molecules present in the cell. At the same time, the high resolution of this technique allows detailed analysis of ribosome density on individual RNAs. Since its invention, the ribosome profiling technique has been utilized in a range of studies in both prokaryotic and eukaryotic organisms. Several studies have adapted and refined the original ribosome profiling protocol for studying specific aspects of translation. Ribosome profiling of initiating ribosomes has been used to map sites of translation initiation. These studies revealed the surprisingly complex organization of translation initiation sites in eukaryotes. Multiple initiation sites are responsible for the generation of N-terminally extended and truncated isoforms of known proteins as well as for the translation of numerous open reading frames (ORFs), upstream of protein coding ORFs. Ribosome profiling of elongating ribosomes has been used for measuring differential gene expression at the level of translation, the identification of novel protein coding genes and ribosome pausing. It has also provided data for developing quantitative models of translation. Although only a dozen or so ribosome profiling datasets have been published so far, they have already dramatically changed our understanding of translational control and have led to new hypotheses regarding the origin of protein coding genes. © 2013 John Wiley & Sons, Ltd. PMID:23696005

  11. Conservation of two distinct types of 100S ribosome in bacteria. (United States)

    Ueta, Masami; Wada, Chieko; Daifuku, Takashi; Sako, Yoshihiko; Bessho, Yoshitaka; Kitamura, Aya; Ohniwa, Ryosuke L; Morikawa, Kazuya; Yoshida, Hideji; Kato, Takayuki; Miyata, Tomoko; Namba, Keiichi; Wada, Akira


    In bacteria, 70S ribosomes (consisting of 30S and 50S subunits) dimerize to form 100S ribosomes, which were first discovered in Escherichia coli. Ribosome modulation factor (RMF) and hibernation promoting factor (HPF) mediate this dimerization in stationary phase. The 100S ribosome is translationally inactive, but it dissociates into two translationally active 70S ribosomes after transfer from starvation to fresh medium. Therefore, the 100S ribosome is called the 'hibernating ribosome'. The gene encoding RMF is found widely throughout the Gammaproteobacteria class, but is not present in any other bacteria. In this study, 100S ribosome formation in six species of Gammaproteobacteria and eight species belonging to other bacterial classes was compared. There were several marked differences between the two groups: (i) Formation of 100S ribosomes was mediated by RMF and short HPF in Gammaproteobacteria species, similar to E. coli, whereas it was mediated only by long HPF in the other bacterial species; (ii) RMF/short HPF-mediated 100S ribosome formation occurred specifically in stationary phase, whereas long HPF-mediated 100S ribosome formation occurred in all growth phases; and (iii) 100S ribosomes formed by long HPF were much more stable than those formed by RMF and short HPF. © 2013 The Authors Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  12. A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy

    NARCIS (Netherlands)

    Franken, Linda; Oostergetel, Gerrit; Pijning, Tjaard; Puri, Pranav; Arkhipova, Valentina Ivanovna; Boekema, Egbert; Poolman, Berend; Guskov, Albert


    Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S

  13. The Ribosomal RNA Genes on Neurospora crassa Mitochrondrial DNA Are Adjacent

    NARCIS (Netherlands)

    Terpstra, P.; Holtrop, M.


    Hybridization of separated 24 S and 17 S ribosomal RNA from Neurospora crassa mitochondrial ribosomes to restriction fragments of mitochondrial DNA leads to the conclusion that the large and small ribosomal RNA are adjacent on the restriction endonuclease cleavage map of the DNA. The distance

  14. Purification and properties of a ribosomal casein kinase from rabbit reticulocytes

    DEFF Research Database (Denmark)

    Issinger, O G


    A casein kinase was isolated and purifed from rabbit reticulocytes. About 90% of the enzyme activity co-sedimented with the ribosomal fraction, whereas about 10% of the enzyme activity was found in the ribosome-free supernatant. Both casein kinases (the ribosome-bound enzyme as well as the free...

  15. Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization

    NARCIS (Netherlands)

    Puri, Pranav; Eckhardt, Thomas H; Franken, Linda E; Fusetti, Fabrizia; Stuart, Marc C A; Boekema, Egbert J; Kuipers, Oscar P; Kok, Jan; Poolman, Berend

    Dimerization and inactivation of ribosomes in Escherichia coli is a two-step process that involves the binding of ribosome modulation factor (RMF) and hibernation promotion factor (HPF). Lactococcus lactisMG1363 expresses a protein, YfiA(Ll), which associates with ribosomes in the stationary phase

  16. Orthogonal least squares based complex-valued functional link network. (United States)

    Amin, Md Faijul; Savitha, Ramasamy; Amin, Muhammad Ilias; Murase, Kazuyuki


    Functional link networks are single-layered neural networks that impose nonlinearity in the input layer using nonlinear functions of the original input variables. In this paper, we present a fully complex-valued functional link network (CFLN) with multivariate polynomials as the nonlinear functions. Unlike multilayer neural networks, the CFLN is free from local minima problem, and it offers very fast learning of parameters because of its linear structure. Polynomial based CFLN does not require an activation function which is a major concern in the complex-valued neural networks. However, it is important to select a smaller subset of polynomial terms (monomials) for faster and better performance since the number of all possible monomials may be quite large. Here, we use the orthogonal least squares (OLS) method in a constructive fashion (starting from lower degree to higher) for the selection of a parsimonious subset of monomials. It is argued here that computing CFLN in purely complex domain is advantageous than in double-dimensional real domain, in terms of number of connection parameters, faster design, and possibly generalization performance. Simulation results on a function approximation, wind prediction with real-world data, and a nonlinear channel equalization problem exhibit that the OLS based CFLN yields very simple structure having favorable performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Magnetocardiogram measured by fundamental mode orthogonal fluxgate array (United States)

    Karo, Hikaru; Sasada, Ichiro


    Magnetocardiography (MCG) of healthy volunteers has been measured by using a fundamental mode orthogonal fluxgate magnetometer array of 32 channels in a magnetic shielded room (MSR). Sensor heads, which are employed, consist of a 45 mm long U-shaped amorphous wire core and a 1000-turn solenoid pick-up coil of 30 mm in length and 3 mm in outer diameter. The excitation current of 100 kHz with large dc bias current is fed directly into wire cores, which are connected in series, whereas the signal detection circuit is provided to each of the sensor heads. A special technique to avoid mutual interaction between sensor heads is implemented, where all the sensor heads are excited synchronously by using a single ac source. A 2-D array having 32 sensors with 4 cm grid spacing was used to measure MCG signals inside an MSR. Measured data from each channel were first filtered (0.16-100 Hz pass band), then averaged for 2 min synchronously with electrocardiogram's peaks taken from both hands. Noise remaining after the average is about 1.8 pTrms for the band-width of 0.16-100 Hz. The QRS complex and the T-wave are clearly detected.

  18. [Quadratic Orthogonal Rotation Combination Design on Alisma orientalis of Fertilization]. (United States)

    Li, Yao; Chen, Xing-fu; Peng, Shi-ming; Liang, Qin; Zhang, Jun; Wu, Chun


    To study the effects of combined N, P, K and micronutrient fertilizers on the yield of Alisma orientalis tuber, and to optimize the fertilizer application rate. Four factors five levels quadratic orthogonal rotation combination design was used. A function was established on nitrogen, phosphor, potassium and microelement fertilizer application rate with the yield of Alisma orientalis tuber. The established mathematical model was of high reliability for prediction with quadratic regression equation of R2 = 0. 8980. The order of increasing Alisma orientalis tuber yield was nitrogen > micronutrient fertilizer > potassium > phosphor. The results of the frequency analysis showed that for the target yield over 8 250 kg/hm2 and the confidence interval of 95%, the optimal fertilizer application rates were as follows :nitrogen of 241. 45 - 283. 55 kg/hm2, phosphor of 81. 14 - 208. 44 kg/hm2, potassium of 95. 57 - 239. 42 kg/hm2, and zinc fertilizer of 14. 32 - 16. 18 kg/hm2, boron fertilizer of 18. 84 - 19. 86 kg/hm2, and molybdenum fertilizer of 0. 151 -0. 159 kg/hm2 in micronutrient fertilizer. Nitrogen is related to the growth of Alisma orientalis, potassium promotes tuber bulking, micronutrient fertilizer consisted of zinc, boron and molybdenum fertilizer promotes Alisma orientalis growth and the absorption of nitrogen, phosphor and potassium. Moderate application of nitrogen, phosphorus, potassium, zinc, boron and molybdenum fertilizer can promote Alisma orientalis tuber yield. The nitrogen has the best effect.

  19. 2D Orthogonal Locality Preserving Projection for Image Denoising. (United States)

    Shikkenawis, Gitam; Mitra, Suman K


    Sparse representations using transform-domain techniques are widely used for better interpretation of the raw data. Orthogonal locality preserving projection (OLPP) is a linear technique that tries to preserve local structure of data in the transform domain as well. Vectorized nature of OLPP requires high-dimensional data to be converted to vector format, hence may lose spatial neighborhood information of raw data. On the other hand, processing 2D data directly, not only preserves spatial information, but also improves the computational efficiency considerably. The 2D OLPP is expected to learn the transformation from 2D data itself. This paper derives mathematical foundation for 2D OLPP. The proposed technique is used for image denoising task. Recent state-of-the-art approaches for image denoising work on two major hypotheses, i.e., non-local self-similarity and sparse linear approximations of the data. Locality preserving nature of the proposed approach automatically takes care of self-similarity present in the image while inferring sparse basis. A global basis is adequate for the entire image. The proposed approach outperforms several state-of-the-art image denoising approaches for gray-scale, color, and texture images.

  20. Aeroelastic System Development Using Proper Orthogonal Decomposition and Volterra Theory (United States)

    Lucia, David J.; Beran, Philip S.; Silva, Walter A.


    This research combines Volterra theory and proper orthogonal decomposition (POD) into a hybrid methodology for reduced-order modeling of aeroelastic systems. The out-come of the method is a set of linear ordinary differential equations (ODEs) describing the modal amplitudes associated with both the structural modes and the POD basis functions for the uid. For this research, the structural modes are sine waves of varying frequency, and the Volterra-POD approach is applied to the fluid dynamics equations. The structural modes are treated as forcing terms which are impulsed as part of the uid model realization. Using this approach, structural and uid operators are coupled into a single aeroelastic operator. This coupling converts a free boundary uid problem into an initial value problem, while preserving the parameter (or parameters) of interest for sensitivity analysis. The approach is applied to an elastic panel in supersonic cross ow. The hybrid Volterra-POD approach provides a low-order uid model in state-space form. The linear uid model is tightly coupled with a nonlinear panel model using an implicit integration scheme. The resulting aeroelastic model provides correct limit-cycle oscillation prediction over a wide range of panel dynamic pressure values. Time integration of the reduced-order aeroelastic model is four orders of magnitude faster than the high-order solution procedure developed for this research using traditional uid and structural solvers.

  1. Orthogonal Procrustes Analysis for Dictionary Learning in Sparse Linear Representation. (United States)

    Grossi, Giuliano; Lanzarotti, Raffaella; Lin, Jianyi


    In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD's robustness and wide applicability.

  2. An improved solution to geometric distortion using an orthogonal method (United States)

    Peng, Huan-Wen; Peng, Qing-Yu; Wang, Na


    The geometric distortion of a CCD field of view has a direct influence on the positional measurements of CCD observations. In order to obtain high precision astrometric results, the geometric distortion should be derived and corrected precisely. As presented in our previous work, a convenient solution has been carried out and has also been applied to observations of Phoebe. In order to further improve the solution, an orthogonal method based on Zernike polynomials is used in this work. Four nights of CCD observations including Himalia, the sixth satellite of Jupiter, and open clusters (NGC 1664 or NGC 2324) on each night have been processed as an application. The observations were obtained from the 2.4 m telescope administered by Yunnan Observatories. The catalog UCAC4 was used to match reference stars in all of the CCD frames. The ephemeris of Himalia is retrieved from the Institut de Mécanique Céleste et de Calcul des Éphémérides (IMCCE). Our results show that the means of observed minus calculated (O-C) positional residuals are -0.034 and -0.026 arcsec in right ascension and declination, respectively. The corresponding standard deviations are {0.031}^{\\prime\\prime } and {0.028}^{\\prime\\prime }. The measurement dispersion is significantly improved compared to that by using our previous solution.

  3. Geometric attributes of retaining glycosyltransferase enzymes favor an orthogonal mechanism.

    Directory of Open Access Journals (Sweden)

    Brock Schuman

    Full Text Available Retaining glycosyltransferase enzymes retain the stereochemistry of the donor glycosidic linkage after transfer to an acceptor molecule. The mechanism these enzymes utilize to achieve retention of the anomeric stereochemistry has been a matter of much debate. Re-analysis of previously released structural data from retaining and inverting glycosyltransferases allows competing mechanistic proposals to be evaluated. The binding of metal-nucleotide-sugars between inverting and retaining enzymes is conformationally unique and requires the donor substrate to occupy two different orientations in the two types of glycosyltransferases. The available structures of retaining glycosyltransferases lack appropriately positioned enzymatic dipolar residues to initiate or stabilize the intermediates of a dissociative mechanism. Further, available structures show that the acceptor nucleophile and anomeric carbon of the donor sugar are in close proximity. Structural features support orthogonal (front-side attack from a position lying ≤ 90° from the C1-O phosphate bond for retaining enzymes. These structural conclusions are consistent with the geometric conclusions of recent kinetic and computational studies.

  4. Orthogonal-like fractional-octave-band filters. (United States)

    Antoni, Jérôme


    This paper addresses the design of digital fractional-octave-band filters with energy conservation and perfect reconstruction--i.e., whose outputs to each fractional-octave-band correctly sum up to the original signal and whose partial energies at each output correctly sum up to the overall signal energy--a combination of properties that cannot be met by any current design despite its considerable importance in many applications. A solution is devised based on the introduction of complex basis functions that span the outputs of the fractional-octave bands and whose real and imaginary parts form two individually--but not mutually--orthogonal bases. This imposes a "partition-of-unity" condition on the design of the filter frequency gains such that they exactly sum up to one over the frequency axis. The practical implementation of the proposed solution uses the discrete Fourier transform, and a fast algorithm is implemented using the fast Fourier transform. The proposed filters are well suited to any application involving the post-processing of finite-energy signals. They closely match the international standard templates, except for a small departure at the bandedge frequencies which can be made arbitrarily small.

  5. Undersampling in Orthogonal Frequency Division Multiplexing Telecommunication Systems

    Directory of Open Access Journals (Sweden)

    Nikos Petrellis


    Full Text Available Several techniques have been proposed that attempt to reconstruct a sparse signal from fewer samples than the ones required by the Nyquist theorem. In this paper, an undersampling technique is presented that allows the reconstruction of the sparse information that is transmitted through Orthogonal Frequency Division Multiplexing (OFDM modulation. The properties of the Discrete Fourier Transform (DFT that is employed by the OFDM modulation, allow the estimation of several samples from others that have already been obtained on the side of the receiver, provided that special relations are valid between the original data values. The inherent sparseness of the original data, as well as the Forward Error Correction (FEC techniques employed, can assist the information recovery from fewer samples. It will be shown that up to 1/4 of the samples can be omitted from the sampling process and substituted by others on the side of the receiver for the successful reconstruction of the original data. In this way, the size of the buffer memory used for sample storage, as well as the storage requirements of the Fast Fourier Transform (FFT implementation at the receiver, may be reduced by up to 25%. The power consumption of the Analog Digital Converter on the side of the receiver is also reduced when a lower sampling rate is used.

  6. Systematic Identification of MCU Modulators by Orthogonal Interspecies Chemical Screening. (United States)

    Arduino, Daniela M; Wettmarshausen, Jennifer; Vais, Horia; Navas-Navarro, Paloma; Cheng, Yiming; Leimpek, Anja; Ma, Zhongming; Delrio-Lorenzo, Alba; Giordano, Andrea; Garcia-Perez, Cecilia; Médard, Guillaume; Kuster, Bernhard; García-Sancho, Javier; Mokranjac, Dejana; Foskett, J Kevin; Alonso, M Teresa; Perocchi, Fabiana


    The mitochondrial calcium uniporter complex is essential for calcium (Ca 2+ ) uptake into mitochondria of all mammalian tissues, where it regulates bioenergetics, cell death, and Ca 2+ signal transduction. Despite its involvement in several human diseases, we currently lack pharmacological agents for targeting uniporter activity. Here we introduce a high-throughput assay that selects for human MCU-specific small-molecule modulators in primary drug screens. Using isolated yeast mitochondria, reconstituted with human MCU, its essential regulator EMRE, and aequorin, and exploiting a D-lactate- and mannitol/sucrose-based bioenergetic shunt that greatly minimizes false-positive hits, we identify mitoxantrone out of more than 600 clinically approved drugs as a direct selective inhibitor of human MCU. We validate mitoxantrone in orthogonal mammalian cell-based assays, demonstrating that our screening approach is an effective and robust tool for MCU-specific drug discovery and, more generally, for the identification of compounds that target mitochondrial functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Orthogonal Procrustes Analysis for Dictionary Learning in Sparse Linear Representation.

    Directory of Open Access Journals (Sweden)

    Giuliano Grossi

    Full Text Available In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD's robustness and wide applicability.

  8. Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation.

    Directory of Open Access Journals (Sweden)

    Mélodie Duval


    Full Text Available Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking of a folded mRNA precedes an accommodation step. Here, we used a combination of experimental approaches in vitro (kinetic of mRNA unfolding and binding experiments to analyze mRNA-protein or mRNA-ribosome complexes, toeprinting assays to follow the formation of ribosomal initiation complexes and in vivo (genetic to monitor the action of ribosomal protein S1 on the initiation of structured and regulated mRNAs. We demonstrate that r-protein S1 endows the 30S with an RNA chaperone activity that is essential for the docking and the unfolding of structured mRNAs, and for the correct positioning of the initiation codon inside the decoding channel. The first three OB-fold domains of S1 retain all its activities (mRNA and 30S binding, RNA melting activity on the 30S subunit. S1 is not required for all mRNAs and acts differently on mRNAs according to the signals present at their 5' ends. This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features.

  9. The Role of Disordered Ribosomal Protein Extensions in the Early Steps of Eubacterial 50 S Ribosomal Subunit Assembly

    Directory of Open Access Journals (Sweden)

    Youri Timsit


    Full Text Available Although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (IUPs remain to be elucidated. This review is focused on the role of the extensions of the ribosomal proteins in the early steps of the assembly of the eubacterial 50 S subunit. The recent crystallographic structures of the ribosomal particles have revealed the picture of a complex assembly pathway that condenses the rRNA and the ribosomal proteins into active ribosomes. However, little is know about the molecular mechanisms of this process. It is thought that the long basic r-protein extensions that penetrate deeply into the subunit cores play a key role through disorder-order transitions and/or co-folding mechanisms. A current view is that such structural transitions may facilitate the proper rRNA folding. In this paper, the structures of the proteins L3, L4, L13, L20, L22 and L24 that have been experimentally found to be essential for the first steps of ribosome assembly have been compared. On the basis of their structural and dynamics properties, three categories of extensions have been identified. Each of them seems to play a distinct function. Among them, only the coil-helix transition that occurs in a phylogenetically conserved cluster of basic residues of the L20 extension appears to be strictly required for the large subunit assembly in eubacteria. The role of a helix-coil transitions in 23 S RNA folding is discussed in the light of the calcium binding protein calmodulin that shares many structural and dynamics properties with L20.

  10. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. (United States)

    Handa, Yoshihiro; Inaho, Noriyuki; Nameki, Nobukazu


    In bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger RNA (tmRNA). In the absence of tmRNA, however, there is evidence that stalled ribosomes are released from non-stop mRNAs. Here, we show a novel ribosome rescue system mediated by a small basic protein, YaeJ, from Escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (RF). In vitro translation experiments using the E. coli-based reconstituted cell-free protein synthesis system revealed that YaeJ can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs containing rare codon clusters that extend downstream from the P-site and prevent Ala-tmRNA•SmpB from entering the empty A-site. In addition, YaeJ had no effect on translation of a normal mRNA with a stop codon. These results suggested a novel tmRNA-independent rescue system for stalled ribosomes in E. coli. YaeJ was almost exclusively found in the 70S ribosome and polysome fractions after sucrose density gradient sedimentation, but was virtually undetectable in soluble fractions. The C-terminal basic residue-rich extension was also found to be required for ribosome binding. These findings suggest that YaeJ functions as a ribosome-attached rescue device for stalled ribosomes.

  11. WSC-07: Evolving the Web Services Challenge

    NARCIS (Netherlands)

    Blake, M. Brian; Cheung, William K.W.; Jaeger, Michael C.; Wombacher, Andreas

    Service-oriented architecture (SOA) is an evolving architectural paradigm where businesses can expose their capabilities as modular, network-accessible software services. By decomposing capabilities into modular services, organizations can share their offerings at multiple levels of granularity

  12. Satcom access in the evolved packet core

    NARCIS (Netherlands)

    Cano, M.D.; Norp, A.H.J.; Popova, M.P.


    Satellite communications (Satcom) networks are increasingly integrating with terrestrial communications networks, namely Next Generation Networks (NGN). In the area of NGN the Evolved Packet Core (EPC) is a new network architecture that can support multiple access technologies. When Satcom is

  13. Acquisition: Acquisition of the Evolved SEASPARROW Missile

    National Research Council Canada - National Science Library


    .... The Evolved SEASPARROW Missile, a Navy Acquisition Category II program, is an improved version of the RIM-7P SEASPARROW missile that will intercept high-speed maneuvering, anti-ship cruise missiles...

  14. Structural variation of the ribosomal gene cluster within the class Insecta

    Energy Technology Data Exchange (ETDEWEB)

    Mukha, D.V.; Sidorenko, A.P.; Lazebnaya, I.V. [Vavilov Institute of General Genetics, Moscow (Russian Federation)] [and others


    General estimation of ribosomal DNA variation within the class Insecta is presented. It is shown that, using blot-hybridization, one can detect differences in the structure of the ribosomal gene cluster not only between genera within an order, but also between species within a genera, including sibling species. Structure of the ribosomal gene cluster of the Coccinellidae family (ladybirds) is analyzed. It is shown that cloned highly conservative regions of ribosomal DNA of Tetrahymena pyriformis can be used as probes for analyzing ribosomal genes in insects. 24 refs., 4 figs.

  15. Influence of mesh non-orthogonality on numerical simulation of buoyant jet flows

    Energy Technology Data Exchange (ETDEWEB)

    Ishigaki, Masahiro, E-mail:; Abe, Satoshi; Sibamoto, Yasuteru; Yonomoto, Taisuke


    Highlights: • Influence of mesh non-orthogonality on numerical solution of buoyant jet flows. • Buoyant jet flows are simulated with hexahedral and prismatic meshes. • Jet instability with prismatic meshes may be overestimated compared to that with hexahedral meshes. • Modified solvers that can reduce the influence of mesh non-orthogonality and reduce computation time are proposed. - Abstract: In the present research, we discuss the influence of mesh non-orthogonality on numerical solution of a type of buoyant flow. Buoyant jet flows are simulated numerically with hexahedral and prismatic mesh elements in an open source Computational Fluid Dynamics (CFD) code called “OpenFOAM”. Buoyant jet instability obtained with the prismatic meshes may be overestimated compared to that obtained with the hexahedral meshes when non-orthogonal correction is not applied in the code. Although the non-orthogonal correction method can improve the instability generated by mesh non-orthogonality, it may increase computation time required to reach a convergent solution. Thus, we propose modified solvers that can reduce the influence of mesh non-orthogonality and reduce the computation time compared to the existing solvers in OpenFOAM. It is demonstrated that calculations for a buoyant jet with a large temperature difference are performed faster by the modified solver.

  16. Cyberspace Operations: Influence Upon Evolving War Theory (United States)



  17. Evolving effective incremental SAT solvers with GP


    Bader, Mohamed; Poli, R.


    Hyper-Heuristics could simply be defined as heuristics to choose other heuristics, and it is a way of combining existing heuristics to generate new ones. In a Hyper-Heuristic framework, the framework is used for evolving effective incremental (Inc*) solvers for SAT. We test the evolved heuristics (IncHH) against other known local search heuristics on a variety of benchmark SAT problems.

  18. Bifunctional Poly(acrylamide) Hydrogels through Orthogonal Coupling Chemistries. (United States)

    Farrukh, Aleeza; Paez, Julieta I; Salierno, Marcelo; Fan, Wenqiang; Berninger, Benedikt; Del Campo, Aránzazu


    Biomaterials for cell culture allowing simple and quantitative presentation of instructive cues enable rationalization of the interplay between cells and their surrounding microenvironment. Poly(acrylamide) (PAAm) hydrogels are popular 2D-model substrates for this purpose. However, quantitative and reproducible biofunctionalization of PAAm hydrogels with multiple ligands in a trustable, controlled, and independent fashion is not trivial. Here, we describe a method for bifunctional modification of PAAm hydrogels with thiol- and amine- containing biomolecules with controlled densities in an independent, orthogonal manner. We developed copolymer networks of AAm with 9% acrylic acid and 2% N-(4-(5-(methylsulfonyl)-1,3,4-oxadiazol-2-yl)phenyl)acrylamide. The covalent binding of thiol- and amine-containing chromophores at tunable concentrations was demonstrated and quantified by UV spectroscopy. The morphology, mechanical properties, and homogeneity of the copolymerized hydrogels were characterized by scanning electron microscopy, dynamic mechanical analysis, and confocal microscopy studies. Our copolymer hydrogels were bifunctionalized with polylysine and a laminin-mimetic peptide using the specific chemistries. We analyzed the effect of binding protocol of the two components in the maturation of cultured postmitotic cortical neurons. Our substrates supported neuronal attachment, proliferation, and neuronal differentiation. We found that neurons cultured on our hydrogels bifunctionalized with ligand-specific chemistries in a sequential fashion exhibited higher maturation at comparable culture times than using a simultaneous bifunctionalization strategy, displaying a higher number of neurites, branches, and dendritic filopodia. These results demonstrate the relevance of quantitative and optimized coupling chemistries for the performance of simple biomaterials and with sensitive cell types.

  19. Superresolution Imaging of Ribosomes and RNA Polymerase in Live Escherichia coli Cells (United States)

    Bakshi, Somenath; Siryaporn, Albert; Goulian, Mark; Weisshaar, James C.


    Summary Quantitative spatial distributions of ribosomes (S2-YFP) and RNA polymerase (β′-yGFP) in live E. coli are measured by superresolution fluorescence microscopy. In moderate growth conditions, Nucleoid-ribosome segregation is strong, and RNAP localizes to the nucleoid lobes. The mean copy numbers per cell are 4600 RNAPs and 55,000 ribosomes. Only 10–15% of the ribosomes lie within the densest part of the nucleoid lobes, and at most 4% of the RNAPs lie in the two ribosome-rich endcaps. The predominant observed diffusion coefficient of ribosomes is Dribo = 0.04 μm2/s, attributed to free mRNA being translated by one or more 70S ribosomes. We find no clear evidence of sub-diffusion, as would arise from tethering of ribosomes. The degree of DNA-ribosome segregation strongly suggests that in E. coli most translation occurs on free mRNA transcripts that have diffused into the ribosome-rich regions. Both RNAP and ribosome radial distributions extend to the cytoplasmic membrane, consistent with the transertion hypothesis. However, few if any RNAP copies lie near the membrane of the endcaps. This suggests that if transertion occurs, it exerts a direct radially expanding force on the nucleoid, but not a direct axially expanding force. PMID:22624875

  20. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction (United States)

    Fritz, Brian R.; Jewett, Michael C.


    In vitro ribosome construction could enable studies of ribosome assembly and function, provide a route toward constructing minimal cells for synthetic biology, and permit the construction of ribosome variants with new functions. Toward these long-term goals, we recently reported on an integrated, one-pot ribosomal RNA synthesis (rRNA), ribosome assembly, and translation technology (termed iSAT) for the construction of Escherichia coli ribosomes in crude ribosome-free S150 extracts. Here, we aimed to improve the activity of iSAT through transcriptional tuning. Specifically, we increased transcriptional efficiency through 3′ modifications to the rRNA gene sequences, optimized plasmid and polymerase concentrations, and demonstrated the use of a T7-promoted rRNA operon for stoichiometrically balanced rRNA synthesis and native rRNA processing. Our modifications produced a 45-fold improvement in iSAT protein synthesis activity, enabling synthesis of 429 ± 15 nmol/l green fluorescent protein in 6 h batch reactions. Further, we show that the translational activity of ribosomes purified from iSAT reactions is about 20% the activity of native ribosomes purified directly from E. coli cells. Looking forward, we believe iSAT will enable unique studies to unravel the systems biology of ribosome biogenesis and open the way to new methods for making and studying ribosomal variants. PMID:24792158

  1. Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data. (United States)

    Wang, Hao; Kingsford, Carl; McManus, C Joel


    Ribosome profiling has emerged as a powerful technique to study mRNA translation. Ribosome profiling has the potential to determine the relative quantities and locations of ribosomes on mRNA genome wide. Taking full advantage of this approach requires accurate measurement of ribosome locations. However, experimental inconsistencies often obscure the positional information encoded in ribosome profiling data. Here, we describe the Ribodeblur pipeline, a computational analysis tool that uses a maximum likelihood framework to infer ribosome positions from heterogeneous datasets. Ribodeblur is simple to install, and can be run on an average modern Mac or Linux-based laptop. We detail the process of applying the pipeline to high-coverage ribosome profiling data in yeast, and discuss important considerations for potential extension to other organisms. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. In vivo labelling of functional ribosomes reveals spatial regulation during starvation in Podospora anserina

    Directory of Open Access Journals (Sweden)

    Silar Philippe


    Full Text Available Abstract Background To date, in eukaryotes, ribosomal protein expression is known to be regulated at the transcriptional and/or translational levels. But other forms of regulation may be possible. Results Here, we report the successful tagging of functional ribosomal particles with a S7-GFP chimaeric protein, making it possible to observe in vivo ribosome dynamics in the filamentous fungus Podospora anserina. Microscopic observations revealed a novel kind of ribosomal protein regulation during the passage between cell growth and stationary phases, with a transient accumulation of ribosomal proteins and/or ribosome subunits in the nucleus, possibly the nucleolus, being observed at the beginning of stationary phase. Conclusion Nuclear sequestration can be another level of ribosomal protein regulation in eukaryotic cells.This may contribute to the regulation of cell growth and division.

  3. Optimization of LED-based non-imaging optics with orthogonal polynomial shapes (United States)

    Brick, Peter; Wiesmann, Christopher


    Starting with a seminal paper by Forbes [1], orthogonal polynomials have received considerable interest as descriptors of lens shapes for imaging optics. However, there is little information on the application of orthogonal polynomials in the field of non-imaging optics. Here, we consider fundamental cases related to LED primary and secondary optics. To make it most realistic, we avoid many of the simplifications of non-imaging theory and consider the full complexity of LED optics. In this framework, the benefits of orthogonal polynomial surface description for LED optics are evaluated in comparison to a surface description by widely used monomials.

  4. An Orthogonal Multi-Swarm Cooperative PSO Algorithm with a Particle Trajectory Knowledge Base

    Directory of Open Access Journals (Sweden)

    Jun Yang


    Full Text Available A novel orthogonal multi-swarm cooperative particle swarm optimization (PSO algorithm with a particle trajectory knowledge base is presented in this paper. Different from the traditional PSO algorithms and other variants of PSO, the proposed orthogonal multi-swarm cooperative PSO algorithm not only introduces an orthogonal initialization mechanism and a particle trajectory knowledge base for multi-dimensional optimization problems, but also conceives a new adaptive cooperation mechanism to accomplish the information interaction among swarms and particles. Experiments are conducted on a set of benchmark functions, and the results show its better performance compared with traditional PSO algorithm in aspects of convergence, computational efficiency and avoiding premature convergence.

  5. Interaction of pleuromutilin derivatives with the ribosomal peptidyl transferase center

    DEFF Research Database (Denmark)

    Long, K. S.; Hansen, L. K.; Jakobsen, L.


    of pleuromutilin-based drugs, the binding of the antibiotic pleuromutilin and three semisynthetic derivatives with different side chain extensions has been investigated using chemical footprinting. The nucleotides A2058, A2059, G2505, and U2506 are affected in all of the footprints, suggesting that the drugs...... are similarly anchored in the binding pocket by the common tricyclic mutilin core. However, varying effects are observed at U2584 and U2585, indicating that the side chain extensions adopt distinct conformations within the cavity and thereby affect the rRNA conformation differently. An Escherichia coli L3......Tiamulin is a pleuromutilin antibiotic that is used in veterinary medicine. The recently published crystal structure of a tiamulin-50S ribosomal subunit complex provides detailed information about how this drug targets the peptidyl transferase center of the ribosome. To promote rational design...

  6. Expression of protein-coding genes embedded in ribosomal DNA

    DEFF Research Database (Denmark)

    Johansen, Steinar D; Haugen, Peik; Nielsen, Henrik


    Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns...... that encode reverse transcriptase-like genes, and group I introns and archaeal introns that encode homing endonuclease genes (HEGs). Although rDNA-embedded protein genes are widespread in nuclei, organelles and bacteria, there is surprisingly little information available on how these genes are expressed....... Exceptions include a handful of HEGs from group I introns. Recent studies have revealed unusual and essential roles of group I and group I-like ribozymes in the endogenous expression of HEGs. Here we discuss general aspects of rDNA-embedded protein genes and focus on HEG expression from group I introns...

  7. Dodecandrin, a new ribosome-inhibiting protein from Phytolacca dodecandra. (United States)

    Ready, M P; Adams, R P; Robertus, J D


    Dodecandrin, a newly discovered ribosome-inhibiting protein, has been isolated and purified from the leaves of the African endod plant, Phytolacca dodecandra. Dodecandrin has a molecular weight of approx. 29 000. It cross-reacts with antiserum prepared against pokeweed antiviral protein from Phytolacca americana and exhibits similar requirements for antiribosomal activity. It is more basic than pokeweed antiviral protein, and comparison of the first 30 amino-terminal residues of the two proteins reveals 83% homology. This level of homology is greater than that between pokeweed antiviral protein and pokeweed antiviral protein S, another antiviral protein found in P. americana. Such conservatism in sequence, coupled with the high efficiency of the proteins in deactivating ribosomes and with their abundance in plant tissue, suggests that they serve an important function in the life of the plant, probably as a defense against infection.

  8. Mechanisms of In Vivo Ribosome Maintenance Change in Response to Nutrient Signals. (United States)

    Mathis, Andrew D; Naylor, Bradley C; Carson, Richard H; Evans, Eric; Harwell, Justin; Knecht, Jared; Hexem, Eric; Peelor, Fredrick F; Miller, Benjamin F; Hamilton, Karyn L; Transtrum, Mark K; Bikman, Benjamin T; Price, John C


    Control of protein homeostasis is fundamental to the health and longevity of all organisms. Because the rate of protein synthesis by ribosomes is a central control point in this process, regulation, and maintenance of ribosome function could have amplified importance in the overall regulatory circuit. Indeed, ribosomal defects are commonly associated with loss of protein homeostasis, aging, and disease (1-4), whereas improved protein homeostasis, implying optimal ribosomal function, is associated with disease resistance and increased lifespan (5-7). To maintain a high-quality ribosome population within the cell, dysfunctional ribosomes are targeted for autophagic degradation. It is not known if complete degradation is the only mechanism for eukaryotic ribosome maintenance or if they might also be repaired by replacement of defective components. We used stable-isotope feeding and protein mass spectrometry to measure the kinetics of turnover of ribosomal RNA (rRNA) and 71 ribosomal proteins (r-proteins) in mice. The results indicate that exchange of individual proteins and whole ribosome degradation both contribute to ribosome maintenance in vivo In general, peripheral r-proteins and those with more direct roles in peptide-bond formation are replaced multiple times during the lifespan of the assembled structure, presumably by exchange with a free cytoplasmic pool, whereas the majority of r-proteins are stably incorporated for the lifetime of the ribosome. Dietary signals impact the rates of both new ribosome assembly and component exchange. Signal-specific modulation of ribosomal repair and degradation could provide a mechanistic link in the frequently observed associations among diminished rates of protein synthesis, increased autophagy, and greater longevity (5, 6, 8, 9). © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus


    Wang, Ruanlin; Xiong, Jie; Wang, Wei; Miao, Wei; Liang, Aihua


    Programmed ?1 ribosomal frameshifting (?1 PRF) has been identified as a mechanism to regulate the expression of many viral genes and some cellular genes. The slippery site of ?1 PRF has been well characterized, whereas the +1 PRF signal and the mechanism involved in +1 PRF remain poorly understood. Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes. To accurately assess the frequency of genes requiring fr...

  10. Ribosome signatures aid bacterial translation initiation site identification. (United States)

    Giess, Adam; Jonckheere, Veronique; Ndah, Elvis; Chyżyńska, Katarzyna; Van Damme, Petra; Valen, Eivind


    While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Utilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome. Signatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites.

  11. A new version of the RDP (Ribosomal Database Project) (United States)

    Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.; hide


    The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW ( The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

  12. The Ribosome Restrains Molten Globule Formation in Stalled Nascent Flavodoxin. (United States)

    Houwman, Joseline A; André, Estelle; Westphal, Adrie H; van Berkel, Willem J H; van Mierlo, Carlo P M


    Folding of proteins usually involves intermediates, of which an important type is the molten globule (MG). MGs are ensembles of interconverting conformers that contain (non-)native secondary structure and lack the tightly packed tertiary structure of natively folded globular proteins. Whereas MGs of various purified proteins have been probed to date, no data are available on their presence and/or effect during protein synthesis. To study whether MGs arise during translation, we use ribosome-nascent chain (RNC) complexes of the electron transfer protein flavodoxin. Full-length isolated flavodoxin, which contains a non-covalently bound flavin mononucleotide (FMN) as cofactor, acquires its native α/β parallel topology via a folding mechanism that contains an off-pathway intermediate with molten globular characteristics. Extensive population of this MG state occurs at physiological ionic strength for apoflavodoxin variant F44Y, in which a phenylalanine at position 44 is changed to a tyrosine. Here, we show for the first time that ascertaining the binding rate of FMN as a function of ionic strength can be used as a tool to determine the presence of the off-pathway MG on the ribosome. Application of this methodology to F44Y apoflavodoxin RNCs shows that at physiological ionic strength the ribosome influences formation of the off-pathway MG and forces the nascent chain toward the native state. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. The Ribosome Restrains Molten Globule Formation in Stalled Nascent Flavodoxin* (United States)

    Houwman, Joseline A.; André, Estelle; Westphal, Adrie H.; van Berkel, Willem J. H.; van Mierlo, Carlo P. M.


    Folding of proteins usually involves intermediates, of which an important type is the molten globule (MG). MGs are ensembles of interconverting conformers that contain (non-)native secondary structure and lack the tightly packed tertiary structure of natively folded globular proteins. Whereas MGs of various purified proteins have been probed to date, no data are available on their presence and/or effect during protein synthesis. To study whether MGs arise during translation, we use ribosome-nascent chain (RNC) complexes of the electron transfer protein flavodoxin. Full-length isolated flavodoxin, which contains a non-covalently bound flavin mononucleotide (FMN) as cofactor, acquires its native α/β parallel topology via a folding mechanism that contains an off-pathway intermediate with molten globular characteristics. Extensive population of this MG state occurs at physiological ionic strength for apoflavodoxin variant F44Y, in which a phenylalanine at position 44 is changed to a tyrosine. Here, we show for the first time that ascertaining the binding rate of FMN as a function of ionic strength can be used as a tool to determine the presence of the off-pathway MG on the ribosome. Application of this methodology to F44Y apoflavodoxin RNCs shows that at physiological ionic strength the ribosome influences formation of the off-pathway MG and forces the nascent chain toward the native state. PMID:27784783

  14. Single Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics (United States)

    Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskarin; Cabral, Diana; Liu, Hanqing; Wang, Yuhong; Zhang, Haibo; Rosenblum, Gabriel; Smilansky, Zeev; Goldman, Yale E.; Cooperman, Barry S.


    We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3 and Cy5 labeled tRNAs. Pre-translocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid complex. EF-G·GTP binding to both hybrid and classical PRE complexes halts these fluctuations prior to catalyzing translocation to form the post-translocation (POST) complex. EF-G dependent translocation from the classical PRE complex proceeds via transient formation of a short-lived hybrid intermediate. A-site binding of either EF-G to the PRE complex or of aminoacyl-tRNA·EF-Tu ternary complex to the POST complex markedly suppresses ribosome conformational lability. PMID:21549313

  15. A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses

    Directory of Open Access Journals (Sweden)

    Xiaolan Huang


    Full Text Available Programmed −1 ribosomal frameshifting (PRF and stop codon readthrough are two translational recoding mechanisms utilized by some RNA viruses to express their structural and enzymatic proteins at a defined ratio. Efficient recoding usually requires an RNA pseudoknot located several nucleotides downstream from the recoding site. To assess the strategic importance of the recoding pseudoknots, we have carried out a large scale genome-wide analysis in which we used an in-house developed program to detect all possible H-type pseudoknots within the genomic mRNAs of 81 animal viruses. Pseudoknots are detected downstream from ~85% of the recoding sites, including many previously unknown pseudoknots. ~78% of the recoding pseudoknots are the most stable pseudoknot within the viral genomes. However, they are not as strong as some designed pseudoknots that exhibit roadblocking effect on the translating ribosome. Strong roadblocking pseudoknots are not detected within the viral genomes. These results indicate that the decoding pseudoknots have evolved to possess optimal stability for efficient recoding. We also found that the sequence at the gag-pol frameshift junction of HIV1 harbors potential elaborated pseudoknots encompassing the frameshift site. A novel mechanism is proposed for possible involvement of the elaborated pseudoknots in the HIV1 PRF event.

  16. Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

    DEFF Research Database (Denmark)

    Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff


    One hallmark of natural organisms is their significant evolvability, i.e.,their increased potential for further evolution. However, reproducing such evolvability in artificial evolution remains a challenge, which both reduces the performance of evolutionary algorithms and inhibits the study...... of evolvable digital phenotypes. Although some types of selection in evolutionary computation indirectly encourage evolvability, one unexplored possibility is to directly select for evolvability. To do so, we estimate an individual's future potential for diversity by calculating the behavioral diversity of its...... immediate offspring, and select organisms with increased offspring variation. While the technique is computationally expensive, we hypothesized that direct selection would better encourage evolvability than indirect methods. Experiments in two evolutionary robotics domains confirm this hypothesis: in both...

  17. Evolved atmospheric entry corridor with safety factor (United States)

    Liang, Zixuan; Ren, Zhang; Li, Qingdong


    Atmospheric entry corridors are established in previous research based on the equilibrium glide condition which assumes the flight-path angle to be zero. To get a better understanding of the highly constrained entry flight, an evolved entry corridor that considers the exact flight-path angle is developed in this study. Firstly, the conventional corridor in the altitude vs. velocity plane is extended into a three-dimensional one in the space of altitude, velocity, and flight-path angle. The three-dimensional corridor is generated by a series of constraint boxes. Then, based on a simple mapping method, an evolved two-dimensional entry corridor with safety factor is obtained. The safety factor is defined to describe the flexibility of the flight-path angle for a state within the corridor. Finally, the evolved entry corridor is simulated for the Space Shuttle and the Common Aero Vehicle (CAV) to demonstrate the effectiveness of the corridor generation approach. Compared with the conventional corridor, the evolved corridor is much wider and provides additional information. Therefore, the evolved corridor would benefit more to the entry trajectory design and analysis.

  18. Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex. (United States)

    Weyer, Felix Alexander; Gumiero, Andrea; Gesé, Genís Valentín; Lapouge, Karine; Sinning, Irmgard


    Cotranslational chaperones assist de novo folding of nascent polypeptides, prevent them from aggregating and modulate translation. The ribosome-associated complex (RAC) is unique in that the Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1 form a stable heterodimer, which acts as a cochaperone for the Hsp70 chaperone Ssb. Here we present the structure of the Chaetomium thermophilum RAC core comprising Ssz1 and the Zuo1 N terminus. We show how the conserved allostery of Hsp70 proteins is abolished and this Hsp70-Hsp40 pair is molded into a functional unit. Zuo1 stabilizes Ssz1 in trans through interactions that in canonical Hsp70s occur in cis. Ssz1 is catalytically inert and cannot adopt the closed conformation, but the substrate binding domain β is completed by Zuo1. Our study offers insights into the coupling of a special Hsp70-Hsp40 pair, which evolved to link protein folding and translation.

  19. Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranes

    National Research Council Canada - National Science Library

    Rossi, Andrea; Moritz, Tobias J; Ratelade, Julien; Verkman, A S


    Aquaporin-4 (AQP4) is a water channel expressed in astrocytes, skeletal muscle and epithelial cells that forms supramolecular aggregates in plasma membranes called orthogonal arrays of particles (OAPs...

  20. A Comparative Study for Orthogonal Subspace Projection and Constrained Energy Minimization

    National Research Council Canada - National Science Library

    Du, Qian; Ren, Hsuan; Chang, Chein-I


    ...: orthogonal subspace projection (OSP) and constrained energy minimization (CEM). It is shown that they are closely related and essentially equivalent provided that the noise is white with large SNR...

  1. Generalized Christoffel-Darboux formula for classical skew-orthogonal polynomials

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Saugata [233 Green Park, Lake-Town, Kolkata-700 055 (India)], E-mail:


    We show that skew-orthogonal functions, defined with respect to Jacobi weight w{sub a,b}(x) = (1 - x){sup a}(1 + x){sup b}, a, b > -1, including the limiting cases of Laguerre (w{sub a}(x) = x{sup a} e{sup -x}, a > -1) and Gaussian weight (w(x)=e{sup -x{sup 2}}), satisfy three-term recursion relation in the quaternion space. From this, we derive generalized Christoffel-Darboux (GCD) formulae for kernel functions arising in the study of the corresponding orthogonal and symplectic ensembles of random 2N x 2N matrices. Using the GCD formulae we calculate the level densities and prove that in the bulk of the spectrum, under appropriate scaling, the eigenvalue correlations are universal. We also provide evidence to show that there exists a mapping between skew-orthogonal functions arising in the study of orthogonal and symplectic ensembles of random matrices.

  2. Orthogonal polarization spectral (OPS) imaging and topographical characteristics of oral squamous cell carcinoma

    NARCIS (Netherlands)

    Lindeboom, Jerome A.; Mathura, Keshen R.; Ince, Can


    Tumor microcirculatory characteristics until now have only been assessed by histological examination of biopsies or invasive imaging technique. The recent introduction of orthogonal polarization spectral (OPS) imaging as a new tool for in vivo visualization of human microcirculation makes it

  3. A novel optimal configuration form redundant MEMS inertial sensors based on the orthogonal rotation method

    National Research Council Canada - National Science Library

    Cheng, Jianhua; Dong, Jinlu; Landry, Jr, Rene; Chen, Daidai


    .... Simulation and experimentation are also conducted, and the results show that the orthogonal rotation configuration has the best reliability, accuracy and fault detection and isolation (FDI) performance when the number of gyros is nine.

  4. A novel optimal configuration form redundant MEMS inertial sensors based on the orthogonal rotation method. (United States)

    Cheng, Jianhua; Dong, Jinlu; Landry, Rene; Chen, Daidai


    In order to improve the accuracy and reliability of micro-electro mechanical systems (MEMS) navigation systems, an orthogonal rotation method-based nine-gyro redundant MEMS configuration is presented. By analyzing the accuracy and reliability characteristics of an inertial navigation system (INS), criteria for redundant configuration design are introduced. Then the orthogonal rotation configuration is formed through a two-rotation of a set of orthogonal inertial sensors around a space vector. A feasible installation method is given for the real engineering realization of this proposed configuration. The performances of the novel configuration and another six configurations are comprehensively compared and analyzed. Simulation and experimentation are also conducted, and the results show that the orthogonal rotation configuration has the best reliability, accuracy and fault detection and isolation (FDI) performance when the number of gyros is nine.

  5. A Novel Optimal Configuration form Redundant MEMS Inertial Sensors Based on the Orthogonal Rotation Method

    Directory of Open Access Journals (Sweden)

    Jianhua Cheng


    Full Text Available In order to improve the accuracy and reliability of micro-electro mechanical systems (MEMS navigation systems, an orthogonal rotation method-based nine-gyro redundant MEMS configuration is presented. By analyzing the accuracy and reliability characteristics of an inertial navigation system (INS, criteria for redundant configuration design are introduced. Then the orthogonal rotation configuration is formed through a two-rotation of a set of orthogonal inertial sensors around a space vector. A feasible installation method is given for the real engineering realization of this proposed configuration. The performances of the novel configuration and another six configurations are comprehensively compared and analyzed. Simulation and experimentation are also conducted, and the results show that the orthogonal rotation configuration has the best reliability, accuracy and fault detection and isolation (FDI performance when the number of gyros is nine.

  6. DC-balanced line encoding for optical labeling scheme using orthogonal modulation

    DEFF Research Database (Denmark)

    Zhang, Jianfeng; Holm-Nielsen, Pablo Villanueva; Chi, Nan


    It is shown both theoretically and experimentally that 8B/10B encoding is an efficient technique to mitigate the inherent modulation crosstalk in optical labeling scheme using orthogonal modulation....

  7. An extended class of orthogonal polynomials defined by a Sturm–Liouville problem

    National Research Council Canada - National Science Library

    Gómez-Ullate, David; Kamran, Niky; Milson, Robert


    ... eigenfunctions of a Sturm–Liouville problem. As opposed to the classical orthogonal polynomial systems, these sequences start with a polynomial of degree one. We denote these polynomials as X 1 -...

  8. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing (United States)

    Church, George M.; Esvelt, Kevin; Mali, Prashant


    Methods of modulating expression of a target nucleic acid in a cell are provided including use of multiple orthogonal Cas9 proteins to simultaneously and independently regulate corresponding genes or simultaneously and independently edit corresponding genes.

  9. Orthogonal rational functions on the unit circle: from the scalar to the matrix case.

    NARCIS (Netherlands)

    Bultheel, A.; Gonzalez-Vera, P.; Hendriksen, E.; Njastad, O.


    Special functions and orthogonal polynomials in particular have been around for centuries. Can you imagine mathematics without trigonometric functions, the exponential function or polynomials? In the twentieth century the emphasis was on special functions satisfying linear differential equations,

  10. A trifunctional linker suitable for conducting three orthogonal click chemistries in one pot. (United States)

    Knall, Astrid-Caroline; Hollauf, Manuel; Saf, Robert; Slugovc, Christian


    The feasibility of a one pot approach for conducting mutually orthogonal thiol-Michael addition, copper catalyzed azide-alkyne and inverse electron demand Diels-Alder click chemistry on a tri-functional substrate was demonstrated.

  11. Internal Ribosome Entry Site-Based Bicistronic In Situ Reporter Assays for Discovery of Transcription-Targeted Lead Compounds. (United States)

    Lang, Liwei; Ding, Han-Fei; Chen, Xiaoguang; Sun, Shi-Yong; Liu, Gang; Yan, Chunhong


    Although transgene-based reporter gene assays have been used to discover small molecules targeting expression of cancer-driving genes, the success is limited due to the fact that reporter gene expression regulated by incomplete cis-acting elements and foreign epigenetic environments does not faithfully reproduce chemical responses of endogenous genes. Here, we present an internal ribosome entry site-based strategy for bicistronically co-expressing reporter genes with an endogenous gene in the native gene locus, yielding an in situ reporter assay closely mimicking endogenous gene expression without disintegrating its function. This strategy combines the CRISPR-Cas9-mediated genome-editing tool with the recombinase-mediated cassette-exchange technology, and allows for rapid development of orthogonal assays for excluding false hits generated from primary screens. We validated this strategy by developing a screening platform for identifying compounds targeting oncogenic eIF4E, and demonstrated that the novel reporter assays are powerful in searching for transcription-targeted lead compounds with high confidence. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Gap-filling meteorological variables with Empirical Orthogonal Functions (United States)

    Graf, Alexander


    Gap-filling or modelling surface-atmosphere fluxes critically depends on an, ideally continuous, availability of their meteorological driver variables, such as e.g. air temperature, humidity, radiation, wind speed and precipitation. Unlike for eddy-covariance-based fluxes, data gaps are not unavoidable for these measurements. Nevertheless, missing or erroneous data can occur in practice due to instrument or power failures, disturbance, and temporary sensor or station dismounting for e.g. agricultural management or maintenance. If stations with similar measurements are available nearby, using their data for imputation (i.e. estimating missing data) either directly, after an elevation correction or via linear regression, is usually preferred over linear interpolation or monthly mean diurnal cycles. The popular implementation of regional networks of (partly low-cost) stations increases both, the need and the potential, for such neighbour-based imputation methods. For repeated satellite imagery, Beckers and Rixen (2003) suggested an imputation method based on empirical orthogonal functions (EOFs). While exploiting the same linear relations between time series at different observation points as regression, it is able to use information from all observation points to simultaneously estimate missing data at all observation points, provided that never all observations are missing at the same time. Briefly, the method uses the ability of the first few EOFs of a data matrix to reconstruct a noise-reduced version of this matrix; iterating missing data points from an initial guess (the column-wise averages) to an optimal version determined by cross-validation. The poster presents and discusses lessons learned from adapting and applying this methodology to station data. Several years of 10-minute averages of air temperature, pressure and humidity, incoming shortwave, longwave and photosynthetically active radiation, wind speed and precipitation, measured by a regional (70 km by

  13. M-Interval Orthogonal Polynomial Estimators with Applications (United States)

    Jaroszewicz, Boguslaw Emanuel

    In this dissertation, adaptive estimators of various statistical nonlinearities are constructed and evaluated. The estimators are based on classical orthogonal polynomials which allows an exact computation of convergence rates. The first part of the dissertation is devoted to the estimation of one- and multi-dimensional probability density functions. The most attractive computationally is the Legendre estimator, which corresponds to the mean square segmented polynomial approximation of a pdf. Exact bounds for two components of the estimation error--deterministic bias and random error--are derived for all the polynomial estimators. The bounds on the bias are functions of the "smoothness" of the estimated pdf as measured by the number of continuous derivatives the pdf possesses. Adaptively estimated the optimum number of orthonormal polynomials minimizes the total error. In the second part, the theory of polynomial estimators is applied to the estimation of derivatives of pdf and regression functions. The optimum detectors for small signals in nongaussian noise, as well as any kind of statistical filtering involving likelihood function, are based on the nonlinearity which is a ratio of the derivative of the pdf and the pdf itself. Several different polynomial estimators of this nonlinearity are developed and compared. The theory of estimation is then extended to the multivariable case. The partial derivative nonlinearity is used for detection of signals in dependent noise. When the dimensionality of the nonlinearity is very large, the transformed Hermite estimators are particularly useful. The estimators can be viewed as two-stage filters: the first stage is a pre -whitening filter optimum in gaussian noise and the second stage is a nonlinear filter, which improves performance in nongaussian noise. Filtering of this type can be applied to predictive coding, nonlinear identification and other estimation problems involving a conditional expected value. In the third

  14. Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles (United States)

    Babiano, Reyes; Badis, Gwenael; Saveanu, Cosmin; Namane, Abdelkader; Doyen, Antonia; Díaz-Quintana, Antonio; Jacquier, Alain; Fromont-Racine, Micheline; de la Cruz, Jesús


    Ribosome biogenesis requires >300 assembly factors in Saccharomyces cerevisiae. Ribosome assembly factors Imp3, Mrt4, Rlp7 and Rlp24 have sequence similarity to ribosomal proteins S9, P0, L7 and L24, suggesting that these pre-ribosomal factors could be placeholders that prevent premature assembly of the corresponding ribosomal proteins to nascent ribosomes. However, we found L7 to be a highly specific component of Rlp7-associated complexes, revealing that the two proteins can bind simultaneously to pre-ribosomal particles. Cross-linking and cDNA analysis experiments showed that Rlp7 binds to the ITS2 region of 27S pre-rRNAs, at two sites, in helix III and in a region adjacent to the pre-rRNA processing sites C1 and E. However, L7 binds to mature 25S and 5S rRNAs and cross-linked predominantly to helix ES7Lb within 25S rRNA. Thus, despite their predicted structural similarity, our data show that Rlp7 and L7 clearly bind at different positions on the same pre-60S particles. Our results also suggest that Rlp7 facilitates the formation of the hairpin structure of ITS2 during 60S ribosomal subunit maturation. PMID:23945946

  15. SuhB is a novel ribosome associated protein that regulates expression of MexXY by modulating ribosome stalling in Pseudomonas aeruginosa. (United States)

    Shi, Jing; Jin, Yongxin; Bian, Ting; Li, Kewei; Sun, Ziyu; Cheng, Zhihui; Jin, Shouguang; Wu, Weihui


    Translation elongation is modulated by various ribosome-binding proteins. Environmental stresses, such as starvation and antibiotics, can cause stalling of bacterial ribosomes, which may alter gene expression through a transcription or translation attenuation mechanism. In Pseudomonas aeruginosa, the expression of MexXY multidrug efflux system, which plays a significant role in resistance against aminoglycoside antibiotics, is controlled by a translation surveillance mechanism. Stalling of ribosome at the PA5471 leader peptide (PA5471.1) mRNA leads to transcription of PA5471, which subsequently up-regulates the expression of MexXY. In this study, we found that mutation in a suhB gene leads to decreased susceptibility to aminoglycosides. Transcriptomic analysis revealed an up-regulation of MexXY and PA5471, which were demonstrated to be responsible for the decreased susceptibility of the suhB mutant. We further demonstrated that PA5471.1 is essential for the up-regulation of PA5471 in the suhB mutant. Co-immunoprecipitation assay revealed an interaction between SuhB and ribosome, suggesting a role of SuhB in translation. Indeed, higher amount of PA5471.1 mRNA was found to associate with ribosome isolated from the suhB mutant, indicating increased ribosome stalling. Therefore, this study identified SuhB as a novel ribosome associated protein that is involved in modulating ribosome activity. © 2015 John Wiley & Sons Ltd.

  16. Thermal entanglement in an orthogonal dimer-plaquette chain with alternating Ising-Heisenberg coupling


    Paulinelli, H. G.; SOUZA, S.M. de; Rojas, Onofre


    In this paper we explore the entanglement in orthogonal dimer-plaquette Ising-Heisenberg chain, assembled between plaquette edges, also known as orthogonal dimer plaquettes. The quantum entanglement properties involving an infinite chain structure are quite important, not only because the mathematical calculation is cumbersome but also because real materials are well represented by infinite chain. Using the local gauge symmetry of this model, we are able to map onto a simple spin-1 like Ising...

  17. Synchronization Control of Orthogonal Coding Multi-Carrier CDMA on Reverse link


    渡辺, 壮一; Watanabe, Soichi


    This paper applies delay time control for a reverse link of orthogonal coding multi-carrier CDMA system. Orthogonal codoing multi-carrier CDMA is a candidate modulation scheme which can offer large capacity and high speed mobile communication systems under a synchronous condition. To combat the synchronous timing error, the delay time control scheme uses delta function preamble signals and adopts closed loop control. The performance of the delay time control scheme is clarified as expanding t...

  18. On Linear Combinations of Two Orthogonal Polynomial Sequences on the Unit Circle

    Directory of Open Access Journals (Sweden)

    Suárez C


    Full Text Available Let be a monic orthogonal polynomial sequence on the unit circle. We define recursively a new sequence of polynomials by the following linear combination: , , . In this paper, we give necessary and sufficient conditions in order to make be an orthogonal polynomial sequence too. Moreover, we obtain an explicit representation for the Verblunsky coefficients and in terms of and . Finally, we show the relation between their corresponding Carathéodory functions and their associated linear functionals.

  19. Amplitude Noise Suppression and Orthogonal Multiplexing Using Injection-Locked Single-Mode VCSEL

    DEFF Research Database (Denmark)

    Lyubopytov, Vladimir; von Lerber, Tuomo; Lassas, Matti


    We experimentally demonstrate BER reduction and orthogonal modulation using an injection locked single-mode VCSEL. It allows us suppressing an amplitude noise of optical signal and/or double the capacity of an information channel.......We experimentally demonstrate BER reduction and orthogonal modulation using an injection locked single-mode VCSEL. It allows us suppressing an amplitude noise of optical signal and/or double the capacity of an information channel....

  20. Characterization theorem for classical orthogonal polynomials on non-uniform lattices: The functional approach


    Foupouagnigni, Mama; Kenfack Nangho, Maurice; Mboutngam, Salifou


    Using the functional approach, we state and prove a characterization theorem for classical orthogonal polynomials on non-uniform lattices (quadratic lattices of a discrete or a q-discrete variable) including the Askey-Wilson polynomials. This theorem proves the equivalence between seven characterization properties, namely the Pearson equation for the linear functional, the second-order divided-difference equation, the orthogonality of the derivatives, the Rodrigues formula, two types of struc...

  1. Orthogonal translation components for the in vivo incorporation of unnatural amino acids (United States)

    Schultz, Peter G.; Xie, Jianming; Zeng, Huaqiang


    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate unnatural amino acids into proteins produced in eubacterial host cells such as E. coli, or in a eukaryotic host such as a yeast cell. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing unnatural amino acids, and translation systems.

  2. Orthogonal Stability of an Additive-quartic Functional Equation in Non-Archimedean Spaces

    Directory of Open Access Journals (Sweden)

    Hassan Azadi Kenary


    Full Text Available Using fixed point method, we prove the Hyers-Ulam stability of the orthogonally additive-quartic functional equation f(2x+y+ f(2x-y=4 f(x+y+ 4 f(x-y + 10 f(x + 14f(-x - 3 f(y-3f(-y for all $x, y$ with $xperp y$, in non-Archimedean Banach spaces. Here $perp$ is the orthogonality in the sense of Rätz.

  3. Application of fast orthogonal search to linear and nonlinear stochastic systems

    DEFF Research Database (Denmark)

    Chon, K H; Korenberg, M J; Holstein-Rathlou, N H


    linear and nonlinear stochastic ARMA model parameters by using a method known as fast orthogonal search, with an extended model containing prediction errors as part of the model estimation process. The extended algorithm uses fast orthogonal search in a two-step procedure in which deterministic terms...... and accurately. The model order selection criteria developed for the extended algorithm are also crucial in obtaining accurate parameter estimates. Several simulated examples are presented to demonstrate the efficacy of the algorithm....

  4. Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes. (United States)

    Ding, Wei; Liu, Wan-Qiu; Jia, Youli; Li, Yongzhen; van der Donk, Wilfred A; Zhang, Qi


    Production of ribosomally synthesized and posttranslationally modified peptides (RiPPs) has rarely been reported in fungi, even though organisms of this kingdom have a long history as a prolific source of natural products. Here we report an investigation of the phomopsins, antimitotic mycotoxins. We show that phomopsin is a fungal RiPP and demonstrate the widespread presence of a pathway for the biosynthesis of a family of fungal cyclic RiPPs, which we term dikaritins. We characterize PhomM as an S-adenosylmethionine-dependent α-N-methyltransferase that converts phomopsin A to an N,N-dimethylated congener (phomopsin E), and show that the methyltransferases involved in dikaritin biosynthesis have evolved differently and likely have broad substrate specificities. Genome mining studies identified eight previously unknown dikaritins in different strains, highlighting the untapped capacity of RiPP biosynthesis in fungi and setting the stage for investigating the biological activities and unknown biosynthetic transformations of this family of fungal natural products.

  5. Refractoriness of hepatitis C virus internal ribosome entry site to processing by Dicer in vivo

    Directory of Open Access Journals (Sweden)

    Boissonneault Vincent


    Full Text Available Abstract Background Hepatitis C virus (HCV is a positive-strand RNA virus harboring a highly structured internal ribosome entry site (IRES in the 5' nontranslated region of its genome. Important for initiating translation of viral RNAs into proteins, the HCV IRES is composed of RNA structures reminiscent of microRNA precursors that may be targeted by the host RNA silencing machinery. Results We report that HCV IRES can be recognized and processed into small RNAs by the human ribonuclease Dicer in vitro. Furthermore, we identify domains II, III and VI of HCV IRES as potential substrates for Dicer in vitro. However, maintenance of the functional integrity of the HCV IRES in response to Dicer overexpression suggests that the structure of the HCV IRES abrogates its processing by Dicer in vivo. Conclusion Our results suggest that the HCV IRES may have evolved to adopt a structure or a cellular context that is refractory to Dicer processing, which may contribute to viral escape of the host RNA silencing machinery.

  6. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

    Jónsson, Björn Þór; Hoover, Amy K.; Risi, Sebastian


    While the success of electronic music often relies on the uniqueness and quality of selected timbres, many musicians struggle with complicated and expensive equipment and techniques to create their desired sounds. Instead, this paper presents a technique for producing novel timbres that are evolved......, CPPNs can theoretically compute any function and can build on those present in traditional synthesizers (e.g. square, sawtooth, triangle, and sine waves functions) to produce completely novel timbres. Evolved with NeuroEvolution of Augmenting Topologies (NEAT), the aim of this paper is to explore...... the space of potential sounds that can be generated through such compositional sound synthesis networks (CSSNs). To study the effect of evolution on subjective appreciation, participants in a listener study ranked evolved timbres by personal preference, resulting in preferences skewed toward the first...

  7. Quantifying evolvability in small biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Mugler, Andrew [COLUMBIA UNIV; Ziv, Etay [COLUMBIA UNIV; Wiggins, Chris H [COLUMBIA UNIV


    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  8. In situ regeneration of bioactive coatings enabled by an evolved Staphylococcus aureus sortase A (United States)

    Ham, Hyun Ok; Qu, Zheng; Haller, Carolyn A.; Dorr, Brent M.; Dai, Erbin; Kim, Wookhyun; Liu, David R.; Chaikof, Elliot L.


    Surface immobilization of bioactive molecules is a central paradigm in the design of implantable devices and biosensors with improved clinical performance capabilities. However, in vivo degradation or denaturation of surface constituents often limits the long-term performance of bioactive films. Here we demonstrate the capacity to repeatedly regenerate a covalently immobilized monomolecular thin film of bioactive molecules through a two-step stripping and recharging cycle. Reversible transpeptidation by a laboratory evolved Staphylococcus aureus sortase A (eSrtA) enabled the rapid immobilization of an anti-thrombogenic film in the presence of whole blood and permitted multiple cycles of film regeneration in vitro that preserved its biological activity. Moreover, eSrtA transpeptidation facilitated surface re-engineering of medical devices in situ after in vivo implantation through removal and restoration film constituents. These studies establish a rapid, orthogonal and reversible biochemical scheme to regenerate selective molecular constituents with the potential to extend the lifetime of bioactive films.

  9. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. (United States)

    Shi, Zhen; Fujii, Kotaro; Kovary, Kyle M; Genuth, Naomi R; Röst, Hannes L; Teruel, Mary N; Barna, Maria


    Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) exists and enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with differential selectivity for translating subpools of transcripts, including those controlling metabolism, cell cycle, and development. As an example, mRNAs enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their efficient translation. Within several of these transcripts, this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Interaction network of the ribosome assembly machinery from a eukaryotic thermophile. (United States)

    Baßler, Jochen; Ahmed, Yasar Luqman; Kallas, Martina; Kornprobst, Markus; Calviño, Fabiola R; Gnädig, Marén; Thoms, Matthias; Stier, Gunter; Ismail, Sherif; Kharde, Satyavati; Castillo, Nestor; Griesel, Sabine; Bastuck, Sonja; Bradatsch, Bettina; Thomson, Emma; Flemming, Dirk; Sinning, Irmgard; Hurt, Ed


    Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm. Here, we cloned almost the entire set (∼180) of ribosome biogenesis factors from the thermophilic fungus Chaetomium thermophilum in order to perform an in-depth analysis of their protein-protein interaction network as well as exploring the suitability of these thermostable proteins for structural studies. First, we performed a systematic screen, testing about 80 factors for crystallization and structure determination. Next, we performed a yeast 2-hybrid analysis and tested about 32,000 binary combinations, which identified more than 1000 protein-protein contacts between the thermophilic ribosome assembly factors. To exemplary verify several of these interactions, we performed biochemical reconstitution with the focus on the interaction network between 90S pre-ribosome factors forming the ctUTP-A and ctUTP-B modules, and the Brix-domain containing assembly factors of the pre-60S subunit. Our work provides a rich resource for biochemical reconstitution and structural analyses of the conserved ribosome assembly machinery from a eukaryotic thermophile. © 2017 The Protein Society.

  11. Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization. (United States)

    Puri, Pranav; Eckhardt, Thomas H; Franken, Linda E; Fusetti, Fabrizia; Stuart, Marc C A; Boekema, Egbert J; Kuipers, Oscar P; Kok, Jan; Poolman, Bert


    Dimerization and inactivation of ribosomes in Escherichia coli is a two-step process that involves the binding of ribosome modulation factor (RMF) and hibernation promotion factor (HPF). Lactococcus lactis MG1363 expresses a protein, YfiA(L) (l) , which associates with ribosomes in the stationary phase of growth and is responsible for dimerization of ribosomes. We show that full-length YfiA(L) (l) is necessary and sufficient for ribosome dimerization in L. lactis but also functions heterologously in vitro with E. coli ribosomes. Deletion of the yfiA gene has no effect on the growth rate but diminishes the survival of L. lactis under energy-starving conditions. The N-terminal domain of YfiA(L) (l) is homologous to HPF from E. coli, whereas the C-terminal domain has no counterpart in E. coli. By assembling ribosome dimers in vitro, we could dissect the roles of the N- and C-terminal domains of YfiA(L) (l) . It is concluded that the dimerization and inactivation of ribosomes in L. lactis and E. coli differ in several cellular and molecular aspects. In addition, two-dimensional maps of dimeric ribosomes from L. lactis obtained by single particle electron microscopy show a marked structural difference in monomer association in comparison to the ribosome dimers in E. coli. © 2013 John Wiley & Sons Ltd.

  12. Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics. (United States)

    Gupta, Ankit; Shah, Priyanka; Haider, Afreen; Gupta, Kirti; Siddiqi, Mohammad Imran; Ralph, Stuart A; Habib, Saman


    Apicomplexan protists such as Plasmodium and Toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast and mitochondrion. A cross-species comparison with other apicomplexan, algal and diatom species revealed compositional differences in apicomplexan organelle ribosomes and identified considerable reduction and divergence with ribosomes of bacteria or characterized organelle ribosomes from other organisms. We assembled structural models of sections of Plasmodium falciparum organellar ribosomes and predicted interactions with translation inhibitory antibiotics. Differences in predicted drug-ribosome interactions with some of the modelled structures suggested specificity of inhibition between the apicoplast and mitochondrion. Our results indicate that Plasmodium and Toxoplasma organellar ribosomes have a unique composition, resulting from the loss of several large and small subunit proteins accompanied by significant sequence and size divergences in parasite orthologues of ribosomal proteins.

  13. Design of Orthogonal Filtered Multitone Modulation Systems and Comparison among Efficient Realizations

    Directory of Open Access Journals (Sweden)

    Andrea M. Tonello


    Full Text Available We address the efficient realization of a filtered multitone (FMT modulation system and its orthogonal design. FMT modulation can be viewed as a Discrete Fourier Transform (DFT modulated filter bank (FB. It generalizes the popular orthogonal frequency division multiplexing (OFDM scheme by deploying frequency confined subchannel pulses. We compare three realizations that have been described by Cvetković and Vetterli (1998, and Weiss and Stewart (2000, and Tonello (2006. A detailed derivation of them is performed in the time-domain via the exploitation of different FB polyphase decompositions. We then consider the design of an orthogonal FMT system and we exploit the third realization which allows simplifying the orthogonal FB design and obtaining a block diagonal system matrix with independent subblocks. A numerical method is then presented to obtain an orthogonal FB with well frequency confined subchannel pulses for arbitrarily large number of subchannels. Several examples of pulses with minimal length are reported and their performance is evaluated in typical multipath fading channels. Finally, we compare the orthogonal FMT system with a cyclically prefixed OFDM system in the IEEE 802.11 wireless LAN channel. In this scenario, FMT with minimal length pulses and single tap subchannel equalization outperforms the OFDM system in achievable rate.

  14. Design of Orthogonal Filtered Multitone Modulation Systems and Comparison among Efficient Realizations

    Directory of Open Access Journals (Sweden)

    Moret Nicola


    Full Text Available Abstract We address the efficient realization of a filtered multitone (FMT modulation system and its orthogonal design. FMT modulation can be viewed as a Discrete Fourier Transform (DFT modulated filter bank (FB. It generalizes the popular orthogonal frequency division multiplexing (OFDM scheme by deploying frequency confined subchannel pulses. We compare three realizations that have been described by Cvetković and Vetterli (1998, and Weiss and Stewart (2000, and Tonello (2006. A detailed derivation of them is performed in the time-domain via the exploitation of different FB polyphase decompositions. We then consider the design of an orthogonal FMT system and we exploit the third realization which allows simplifying the orthogonal FB design and obtaining a block diagonal system matrix with independent subblocks. A numerical method is then presented to obtain an orthogonal FB with well frequency confined subchannel pulses for arbitrarily large number of subchannels. Several examples of pulses with minimal length are reported and their performance is evaluated in typical multipath fading channels. Finally, we compare the orthogonal FMT system with a cyclically prefixed OFDM system in the IEEE 802.11 wireless LAN channel. In this scenario, FMT with minimal length pulses and single tap subchannel equalization outperforms the OFDM system in achievable rate.

  15. Evolution of evolvability in gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Anton Crombach

    Full Text Available Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question. An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time. Our work demonstrates that long-term evolution of complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations. We show that the population evolves towards genotype-phenotype mappings that allow for an orchestrated network-wide change in the gene expression pattern, requiring only a few specific gene indels. The genes involved are hubs of the networks, or directly influencing the hubs. Moreover, throughout the evolutionary trajectory the networks maintain their mutational robustness. In other words, evolution in an alternating environment leads to a network that is sensitive to a small class of beneficial mutations, while the majority of mutations remain neutral: an example of evolution of evolvability.

  16. RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel. (United States)

    Yoshida, Hideji; Yamamoto, Hiroshi; Uchiumi, Toshio; Wada, Akira


    In gram-negative bacteria such as Escherichia coli, protein synthesis is suppressed by the formation of 100S ribosomes under stress conditions. The 100S ribosome, a dimer of 70S ribosomes, is formed by ribosome modulation factor (RMF) binding to the 70S ribosomes. During the stationary phase, most of the 70S ribosomes turn to 100S ribosomes, which have lost translational activity. This 100S formation is called the hibernation process in the ribosome cycle of the stationary phase. If stationary phase cells are transferred to fresh medium, the 100S ribosomes immediately go back to active 70S ribosomes, showing that inactive 100S active 70S interconversion is a major system regulating translation activity in stationary phase cells. To elucidate the mechanisms of translational inactivation, the binding sites of RMF on 23S rRNA in 100S ribosome of E. coli were examined by a chemical probing method using dimethyl sulphate (DMS). As the results, the nine bases in 23S rRNA were protected from DMS modifications and the modification of one base was enhanced. Interestingly A2451 is included among the protected bases, which is thought to be directly involved in peptidyl transferase activity. We conclude that RMF inactivates ribosomes by covering the peptidyl transferase (PTase) centre and the entrance of peptide exit tunnel. It is surprising that the cell itself produces a protein that seems to inhibit protein synthesis in a similar manner to antibiotics and that it can reversibly bind to and release from the ribosome in response to environmental conditions.

  17. How the first biopolymers could have evolved. (United States)

    Abkevich, V I; Gutin, A M; Shakhnovich, E I


    In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution. PMID:8570645

  18. Evolving Intelligent Systems Methodology and Applications

    CERN Document Server

    Angelov, Plamen; Kasabov, Nik


    From theory to techniques, the first all-in-one resource for EIS. There is a clear demand in advanced process industries, defense, and Internet and communication (VoIP) applications for intelligent yet adaptive/evolving systems. Evolving Intelligent Systems is the first self- contained volume that covers this newly established concept in its entirety, from a systematic methodology to case studies to industrial applications. Featuring chapters written by leading world experts, it addresses the progress, trends, and major achievements in this emerging research field, with a strong emphasis on th

  19. Disruption of ribosome assembly in yeast blocks cotranscriptional pre-rRNA processing and affects the global hierarchy of ribosome biogenesis. (United States)

    Talkish, Jason; Biedka, Stephanie; Jakovljevic, Jelena; Zhang, Jingyu; Tang, Lan; Strahler, John R; Andrews, Philip C; Maddock, Janine R; Woolford, John L


    In higher eukaryotes, pre-rRNA processing occurs almost exclusively post-transcriptionally. This is not the case in rapidly dividing yeast, as the majority of nascent pre-rRNAs are processed cotranscriptionally, with cleavage at the A2 site first releasing a pre-40S ribosomal subunit followed by release of a pre-60S ribosomal subunit upon transcription termination. Ribosome assembly is driven in part by hierarchical association of assembly factors and r-proteins. Groups of proteins are thought to associate with pre-ribosomes cotranscriptionally during early assembly steps, whereas others associate later, after transcription is completed. Here we describe a previously uncharacterized phenotype observed upon disruption of ribosome assembly, in which normally late-binding proteins associate earlier, with pre-ribosomes containing 35S pre-rRNA. As previously observed by many other groups, we show that disruption of 60S subunit biogenesis results in increased amounts of 35S pre-rRNA, suggesting that a greater fraction of pre-rRNAs are processed post-transcriptionally. Surprisingly, we found that early pre-ribosomes containing 35S pre-rRNA also contain proteins previously thought to only associate with pre-ribosomes after early pre-rRNA processing steps have separated maturation of the two subunits. We believe the shift to post-transcriptional processing is ultimately due to decreased cellular division upon disruption of ribosome assembly. When cells are grown under stress or to high density, a greater fraction of pre-rRNAs are processed post-transcriptionally and follow an alternative processing pathway. Together, these results affirm the principle that ribosome assembly occurs through different, parallel assembly pathways and suggest that there is a kinetic foot-race between the formation of protein binding sites and pre-rRNA processing events. © 2016 Talkish et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  20. Involvement of ribosomal protein L6 in assembly of functional 50S ribosomal subunit in Escherichia coli cells

    Energy Technology Data Exchange (ETDEWEB)

    Shigeno, Yuta [Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567 (Japan); Uchiumi, Toshio [Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181 (Japan); Nomura, Takaomi, E-mail: [Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567 (Japan)


    Ribosomal protein L6, an essential component of the large (50S) subunit, primarily binds to helix 97 of 23S rRNA and locates near the sarcin/ricin loop of helix 95 that directly interacts with GTPase translation factors. Although L6 is believed to play important roles in factor-dependent ribosomal function, crucial biochemical evidence for this hypothesis has not been obtained. We constructed and characterized an Escherichia coli mutant bearing a chromosomal L6 gene (rplF) disruption and carrying a plasmid with an arabinose-inducible L6 gene. Although this ΔL6 mutant grew more slowly than its wild-type parent, it proliferated in the presence of arabinose. Interestingly, cell growth in the absence of arabinose was biphasic. Early growth lasted only a few generations (LI-phase) and was followed by a suspension of growth for several hours (S-phase). This suspension was followed by a second growth phase (LII-phase). Cells harvested at both LI- and S-phases contained ribosomes with reduced factor-dependent GTPase activity and accumulated 50S subunit precursors (45S particles). The 45S particles completely lacked L6. Complete 50S subunits containing L6 were observed in all growth phases regardless of the L6-depleted condition, implying that the ΔL6 mutant escaped death because of a leaky expression of L6 from the complementing plasmid. We conclude that L6 is essential for the assembly of functional 50S subunits at the late stage. We thus established conditions for the isolation of L6-depleted 50S subunits, which are essential to study the role of L6 in translation. - Highlights: • We constructed an in vivo functional assay system for Escherichia coli ribosomal protein L6. • Growth of an E. coli ΔL6 mutant was biphasic when L6 levels were depleted. • The ΔL6 mutant accumulated 50S ribosomal subunit precursors that sedimented at 45S. • L6 is a key player in the late stage of E. coli 50S subunit assembly.

  1. Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials

    Directory of Open Access Journals (Sweden)

    Claus Vogl


    Full Text Available In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, DNA consists of two long strands of nucleotides or sites that pair via the complementary bases cytosine and guanine (C and G, on the one hand, and adenine and thymine (A and T, on the other. With whole genome sequencing, most genomic information stored in the DNA has become available for multiple individuals of one or more populations, at least in humans and model species, such as fruit flies of the genus Drosophila. In a genome-wide sample of L sites for M (haploid individuals, the state of each site may be made binary, by binning the complementary bases, e.g., C with G to C/G, and contrasting C/G to A/T, to obtain a “site frequency spectrum” (SFS. Two such samples of either a single population from different time-points or two related populations from a single time-point are called joint site frequency spectra (joint SFS. While mathematical models describing the interplay of mutation, drift and selection have been available for more than 80 years, calculation of exact likelihoods from joint SFS is difficult. Sufficient statistics for inference of, e.g., mutation or selection parameters that would make use of all the information in the genomic data are rarely available. Hence, often suites of crude summary statistics are combined in simulation-based computational approaches. In this article, we use a bi-allelic boundary-mutation and drift population genetic model to compute the transition probabilities of joint SFS using orthogonal polynomials. This allows inference of population genetic parameters, such as the mutation rate (scaled by the population size and the time separating the two samples. We apply this inference method to a population dataset of neutrally-evolving short intronic sites from six DNA sequences of the fruit fly Drosophila melanogaster and the reference

  2. Time-Dependent Impurity in Ultracold Fermions: Orthogonality Catastrophe and Beyond

    Directory of Open Access Journals (Sweden)

    Michael Knap


    Full Text Available The recent experimental realization of strongly imbalanced mixtures of ultracold atoms opens new possibilities for studying impurity dynamics in a controlled setting. In this paper, we discuss how the techniques of atomic physics can be used to explore new regimes and manifestations of Anderson’s orthogonality catastrophe (OC, which could not be accessed in solid-state systems. Specifically, we consider a system of impurity atoms, localized by a strong optical-lattice potential, immersed in a sea of itinerant Fermi atoms. We point out that the Ramsey-interference-type experiments with the impurity atoms allow one to study the OC in the time domain, while radio-frequency (RF spectroscopy probes the OC in the frequency domain. The OC in such systems is universal, not only in the long-time limit, but also for all times and is determined fully by the impurity-scattering length and the Fermi wave vector of the itinerant fermions. We calculate the universal Ramsey response and RF-absorption spectra. In addition to the standard power-law contributions, which correspond to the excitation of multiple particle-hole pairs near the Fermi surface, we identify a novel, important contribution to the OC that comes from exciting one extra particle from the bottom of the itinerant band. This contribution gives rise to a nonanalytic feature in the RF-absorption spectra, which shows a nontrivial dependence on the scattering length, and evolves into a true power-law singularity with the universal exponent 1/4 at the unitarity. We extend our discussion to spin-echo-type experiments, and show that they probe more complicated nonequilibirum dynamics of the Fermi gas in processes in which an impurity switches between states with different interaction strength several times; such processes play an important role in the Kondo problem, but remained out of reach in the solid-state systems. We show that, alternatively, the OC can be seen in the energy-counting statistics

  3. Preface: evolving rotifers, evolving science: Proceedings of the XIV International Rotifer Symposium

    Czech Academy of Sciences Publication Activity Database

    Devetter, Miloslav; Fontaneto, D.; Jersabek, Ch.D.; Welch, D.B.M.; May, L.; Walsh, E.J.


    Roč. 796, č. 1 (2017), s. 1-6 ISSN 0018-8158 Institutional support: RVO:60077344 Keywords : evolving rotifers * 14th International Rotifer Symposium * evolving science Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.056, year: 2016

  4. Thermal and Evolved-Gas Analyzer Illustration (United States)


    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  5. Apollo 16 Evolved Lithology Sodic Ferrogabbro (United States)

    Zeigler, Ryan; Jolliff, B. L.; Korotev, R. L.


    Evolved lunar igneous lithologies, often referred to as the alkali suite, are a minor but important component of the lunar crust. These evolved samples are incompatible-element rich samples, and are, not surprisingly, most common in the Apollo sites in (or near) the incompatible-element rich region of the Moon known as the Procellarum KREEP Terrane (PKT). The most commonly occurring lithologies are granites (A12, A14, A15, A17), monzogabbro (A14, A15), alkali anorthosites (A12, A14), and KREEP basalts (A15, A17). The Feldspathic Highlands Terrane is not entirely devoid of evolved lithologies, and rare clasts of alkali gabbronorite and sodic ferrogabbro (SFG) have been identified in Apollo 16 station 11 breccias 67915 and 67016. Curiously, nearly all pristine evolved lithologies have been found as small clasts or soil particles, exceptions being KREEP basalts 15382/6 and granitic sample 12013 (which is itself a breccia). Here we reexamine the petrography and geochemistry of two SFG-like particles found in a survey of Apollo 16 2-4 mm particles from the Cayley Plains 62283,7-15 and 62243,10-3 (hereafter 7-15 and 10-3 respectively). We will compare these to previously reported SFG samples, including recent analyses on the type specimen of SFG from lunar breccia 67915.

  6. Theoretical estimate of the effect of thermal agitation on ribosome motion generated by stochastic microswimming. (United States)

    González-García, José S


    The effect of thermal agitation on ribosome motion is evaluated through the Péclet number, assuming that the ribosome is self-propelled along the mRNA during protein synthesis by a swimming stroke consisting of a cycle of stochastically-generated ribosome configurations involving its two subunits. The ribosome velocity probability distribution function is obtained, giving an approximately normal distribution. Its mean and variance together with an estimate of the in vivo free diffusion coefficient of the ribosome and using only configuration changes of small size, give a Péclet number similar to motor proteins and microorganisms. These results suggest the feasibility of the stochastic microswimming hypothesis to explain ribosome motion. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Control of ribosome traffic by position-dependent choice of synonymous codons

    DEFF Research Database (Denmark)

    Mitarai, Namiko; Pedersen, Steen


    Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino...... acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby...... ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated...

  8. Monitoring closed head injury induced changes in brain physiology with orthogonal diffuse near-infrared reflectance spectroscopy (United States)

    Abookasis, David; Shochat, Ariel; Mathews, Marlon S.


    We applied an orthogonal diffuse reflectance spectroscopy (o-DRS) to assess brain physiology following closed head injury (CHI). CHI was induced in anesthetized male mice by weight-drop device using ~50gram cylindrical metal falling from a height of 90 cm onto the intact scalp. A total of twenty-six mice were used in the experiments divided randomly into three groups as follows: Group 1 (n=11) consisted of injured mice monitored for 1 hour every 10 minutes. Group 2 (n=10) were the control mice not experience CHI. Group 3 (n=5) consisted of injured mice monitored every minute up to 20 minutes. Measurement of optical quantities of brain tissue (absorption and reduced scattering coefficients) in the near-infrared window from 650 to 1000 nm were carried out by employing different source-detector distances and locations to provide depth sensitivity. With respect to baseline, we found difference in brain hemodynamic properties following injury. In addition, o-DRS successfully evaluate the structural variations likely from evolving cerebral edema throughout exploring the scattering spectral shape.

  9. An x-ray diffraction study of ribosome structure. (United States)

    Dolgov, A D; Ivanov, D A; Kapitonova, K A; Mokul'skii, M A


    Dense gels of E. coli 70 S ribosomes, their 50 S subunits, CM-like particles, RNP strands and their fragments, 38 S particles obtained from RNP strand folding upon addition of Mg2+ ions, and of unoriented salt-free and free rRNA sodium and magnesium salts were studied by X-ray diffraction. It was shown that under dense gel conditions RNA molecules contained in ribosomes unfolded by desalting, like all other particles considered here, have helical regions. Under these conditions free desalted RNA has no helical regions. Experimental data on X-ray scattering at medium angles were compared with the diffraction curves calculated for homogeneous prolate and oblate ellipsoids, for various ellipsoids containing a dense region or an internal cavity, and for ellipsoids containing internal periodic regions. The results indicate that the internal structure of the 50 S ribosome is periodic, i. e., its components form a periodic lattice. The lattice spacings are approximately 42 and 28 A with a 0.8g/g dry weight sample water content. When the 50 S particle water content drops below 0.2 g/g dry weight the periodic structure is disrupted. This disruption is reversible. It was shown that CM-like particles at high ionic strenght (2 M LiCl) have approximately the same internal periodicity as the 50 S particles, but in contrast they lose this periodicity at low ionic strength (10-2M tris-HCl and 5-10-3 M MgCl2).

  10. Requirement of Neuronal Ribosome Synthesis for Growth and Maintenance of the Dendritic Tree. (United States)

    Slomnicki, Lukasz P; Pietrzak, Maciej; Vashishta, Aruna; Jones, James; Lynch, Nicholas; Elliot, Shane; Poulos, Eric; Malicote, David; Morris, Bridgit E; Hallgren, Justin; Hetman, Michal


    The nucleolus serves as a principal site of ribosome biogenesis but is also implicated in various non-ribosomal functions, including negative regulation of the pro-apoptotic transcription factor p53. Although disruption of the nucleolus may trigger the p53-dependent neuronal death, neurotoxic consequences of a selective impairment of ribosome production are unclear. Here, we report that in rat forebrain neuronal maturation is associated with a remarkable expansion of ribosomes despite postnatal down-regulation of ribosomal biogenesis. In cultured rat hippocampal neurons, inhibition of the latter process by knockdowns of ribosomal proteins S6, S14, or L4 reduced ribosome content without disrupting nucleolar integrity, cell survival, and signaling responses to the neurotrophin brain-derived neurotrophic factor. Moreover, reduced general protein synthesis and/or formation of RNA stress granules suggested diminished ribosome recruitment to at least some mRNAs. Such a translational insufficiency was accompanied by impairment of brain-derived neurotrophic factor-mediated dendritic growth. Finally, RNA stress granules and smaller dendritic trees were also observed when ribosomal proteins were depleted from neurons with established dendrites. Thus, a robust ribosomal apparatus is required to carry out protein synthesis that supports dendritic growth and maintenance. Consequently, deficits of ribosomal biogenesis may disturb neurodevelopment by reducing neuronal connectivity. Finally, as stress granule formation and dendritic loss occur early in neurodegenerative diseases, disrupted homeostasis of ribosomes may initiate and/or amplify neurodegeneration-associated disconnection of neuronal circuitries. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Ribosomal Competence and Spore Germination in Fusarium solani (United States)

    Rado, Thomas A.; Cochrane, Vincent W.


    Extracts prepared from macroconidia of Fusarium solani f. sp. phaseoli are capable, under defined conditions, of incorporating phenylalanine into polypeptide with exogenous polyuridylic acid as messenger. Extracts from ungerminated and germinated spores have approximately the same activity. With endogenous template, leucine incorporation occurs, but in this reaction extracts from germinated spores have about 10 times more activity than do those from ungerminated spores. It is suggested that the low rate in ungerminated spores is attributable to a relative deficiency in the number of ribosomes which are organized into polysomes. PMID:5573727

  12. Specialized yeast ribosomes: a customized tool for selective mRNA translation.

    Directory of Open Access Journals (Sweden)

    Johann W Bauer

    Full Text Available Evidence is now accumulating that sub-populations of ribosomes - so-called specialized ribosomes - can favour the translation of subsets of mRNAs. Here we use a large collection of diploid yeast strains, each deficient in one or other copy of the set of ribosomal protein (RP genes, to generate eukaryotic cells carrying distinct populations of altered 'specialized' ribosomes. We show by comparative protein synthesis assays that different heterologous mRNA reporters based on luciferase are preferentially translated by distinct populations of specialized ribosomes. These mRNAs include reporters carrying premature termination codons (PTC thus allowing us to identify specialized ribosomes that alter the efficiency of translation termination leading to enhanced synthesis of the wild-type protein. This finding suggests that these strains can be used to identify novel therapeutic targets in the ribosome. To explore this further we examined the translation of the mRNA encoding the extracellular matrix protein laminin β3 (LAMB3 since a LAMB3-PTC mutant is implicated in the blistering skin disease Epidermolysis bullosa (EB. This screen identified specialized ribosomes with reduced levels of RP L35B as showing enhanced synthesis of full-length LAMB3 in cells expressing the LAMB3-PTC mutant. Importantly, the RP L35B sub-population of specialized ribosomes leave both translation of a reporter luciferase carrying a different PTC and bulk mRNA translation largely unaltered.

  13. Role of the yeast Rrp1 protein in the dynamics of pre-ribosome maturation (United States)



    The Saccharomyces cerevisiae gene RRP1 encodes an essential, evolutionarily conserved protein necsessary for biogenesis of 60S ribosomal subunits. Processing of 27S pre-ribosomal RNA to mature 25S rRNA is blocked and 60S subunits are deficient in the temperature-sensitive rrp1-1 mutant. We have used recent advances in proteomic analysis to examine in more detail the function of Rrp1p in ribosome biogenesis. We show that Rrp1p is a nucleolar protein associated with several distinct 66S pre-ribosomal particles. These pre-ribosomes contain ribosomal proteins plus at least 28 nonribosomal proteins necessary for production of 60S ribosomal subunits. Inactivation of Rrp1p inhibits processing of 27SA3 to 27SBS pre-rRNA and of 27SB pre-rRNA to 7S plus 25.5S pre-rRNA. Thus, in the rrp1-1 mutant, 66S pre-ribosomal particles accumulate that contain 27SA3 and 27SBL pre-ribosomal RNAs. PMID:15100437

  14. Modeling of ribosome dynamics on a ds-mRNA under an external load (United States)

    Shakiba, Bahareh; Dayeri, Maryam; Mohammad-Rafiee, Farshid


    Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.

  15. Modeling of Ribosome Dynamics on a ds-mRNA under an External Load

    CERN Document Server

    Shakiba, Bahareh; Mohammad-Rafiee, Farshid


    Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force, and translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.

  16. Specialized ribosomes: a new frontier in gene regulation and organismal biology (United States)

    Xue, Shifeng; Barna, Maria


    Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than intrinsic regulatory capacity in mRNA translation. However, emerging studies reveal that ribosome activity may be highly regulated. Heterogeneity in ribosome composition resulting from differential expression and post-translational modifications of ribosomal proteins, ribosomal RNA (rRNA) diversity and the activity of ribosome-associated factors may generate ‘specialized ribosomes’ that have a substantial impact on how the genomic template is translated into functional proteins. Moreover, constitutive components of the ribosome may also exert more specialized activities by virtue of their interactions with specific mRNA regulatory elements such as internal ribosome entry sites (IRESs) or upstream open reading frames (uORFs). Here we discuss the hypothesis that intrinsic regulation by the ribosome acts to selectively translate subsets of mRNAs harbouring unique cis-regulatory elements, thereby introducing an additional level of regulation in gene expression and the life of an organism. PMID:22617470

  17. Modeling of ribosome dynamics on a ds-mRNA under an external load. (United States)

    Shakiba, Bahareh; Dayeri, Maryam; Mohammad-Rafiee, Farshid


    Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.

  18. Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. (United States)

    Fischer, Niels; Konevega, Andrey L; Wintermeyer, Wolfgang; Rodnina, Marina V; Stark, Holger


    The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.

  19. Single molecule imaging of the trans-translation entry process via anchoring of the tagged ribosome. (United States)

    Zhou, Zhan-Ping; Shimizu, Yoshihiro; Tadakuma, Hisashi; Taguchi, Hideki; Ito, Koichi; Ueda, Takuya


    Trans-translation is an eubacterial quality control system to rescue the stalled ribosome, in which multiple components such as transfer messenger RNA (tmRNA) and Small protein B (SmpB) are involved. However, how these molecules interact with ribosome remains elusive. Here, we report the single molecule analysis of the trans-translation process. We developed a new method to label the functional ribosome, in which a tag protein (the HaloTag protein of 297 amino acids) was fused to the 30S ribosomal protein S2 and covalently labelled with specific ligand (HaloTag ligand), resulting in the stable and specific labelling of ribosome. Ribosomes were anchored onto the glass surface using biotinylated derivative of the Cy3 HaloTag ligand (i.e. biotin-Cy3-ligand), and real-time interactions of Cy5-tmRNA/SmpB/EF-Tu ternary complexes with anchored ribosomes are observed as a model of the trans-translation entry. Statistical analysis revealed that Cy5-tmRNA/SmpB/EF-Tu ternary complexes bind to the anchored ribosome with the second-order rate constant of 2.6 × 10(6) (1/M/s) and tmRNAs undergo multi-modal pathway before release from ribosome. The methods presented here are also applicable to the analysis for general translation processes.

  20. Tagging of functional ribosomes in living cells by HaloTag® technology. (United States)

    Gallo, Simone; Beugnet, Anne; Biffo, Stefano


    Ribosomal proteins and ribosomal associated proteins are complicated subjects to target and study because of their high conservation through evolution which led to highly structured and regulated proteins. Tagging of ribosomal proteins may allow following of protein synthesis in vivo and isolating translated mRNAs. HaloTag® is a new technology which allows detection in living cells, biochemical purification, and localization studies. In the present work, we tested HaloTag®-based ribosomal tagging. We focused on eIF6 (eukaryotic Initiation Factor 6 free 60S ribosomal marker), RACK1 (Receptor for Activated C Kinase 1; 40S and polysomes, not nuclear), and rpS9 (40S ribosomes, both in the nucleus and in the cytoplasm). Experiments performed on HEK293 cells included ribosomal profiles and Western blot on the fractions, purification of HaloTag® proteins, and fluorescence with time-lapse microscopy. We show that tagged proteins can be incorporated on ribosomes and followed by time-lapse microscopy. eIF6 properly accumulates in the nucleolus, and it is redistributed upon actinomycin D treatment. RACK1 shows a specific cytoplasmic localization, whereas rpS9 is both nucleolar and cytoplasmic. However, efficiency of purification varies due to steric hindrances. In addition, the level of overexpression and degradation may vary upon different constructs. In summary, HaloTag® technology is highly suitable to ribosome tagging, but requires prior characterization for each construct.