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Sample records for adequate selenocysteine trna

  1. Mouse Models Targeting Selenocysteine tRNA Expression for Elucidating the Role of Selenoproteins in Health and Development

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    Dolph L. Hatfield

    2009-09-01

    Full Text Available Selenium (Se deficiency has been known for many years to be associated with disease, impaired growth and a variety of other metabolic disorders in mammals. Only recently has the major role that Se-containing proteins, designated selenoproteins, play in many aspects of health and development begun to emerge. Se is incorporated into protein by way of the Se-containing amino acid, selenocysteine (Sec. The synthesis of selenoproteins is dependent on Sec tRNA for insertion of Sec, the 21st amino acid in the genetic code, into protein. We have taken advantage of this dependency to modulate the expression of Sec tRNA that in turn modulates the expression of selenoproteins by generating transgenic, conditional knockout, transgenic/standard knockout and transgenic/conditional knockout mouse models, all of which involve the Sec tRNA gene, to elucidate the intracellular roles of this protein class.

  2. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

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    Oleg M Ganichkin

    Full Text Available BACKGROUND: Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood. METHODOLOGY/PRINCIPAL FINDINGS: We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec. CONCLUSIONS/SIGNIFICANCE: We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  3. Osteo-chondroprogenitor-specific deletion of the selenocysteine tRNA gene, Trsp, leads to chondronecrosis and abnormal skeletal development: a putative model for Kashin-Beck disease.

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    Charlene M Downey

    2009-08-01

    Full Text Available Kashin-Beck disease, a syndrome characterized by short stature, skeletal deformities, and arthropathy of multiple joints, is highly prevalent in specific regions of Asia. The disease has been postulated to result from a combination of different environmental factors, including contamination of barley by mold mycotoxins, iodine deficiency, presence of humic substances in drinking water, and, importantly, deficiency of selenium. This multifunctional trace element, in the form of selenocysteine, is essential for normal selenoprotein function, including attenuation of excessive oxidative stress, and for the control of redox-sensitive molecules involved in cell growth and differentiation. To investigate the effects of skeletal selenoprotein deficiency, a Cre recombinase transgenic mouse line was used to trigger Trsp gene deletions in osteo-chondroprogenitors. Trsp encodes selenocysteine tRNA([Ser]Sec, required for the incorporation of selenocysteine residues into selenoproteins. The mutant mice exhibited growth retardation, epiphyseal growth plate abnormalities, and delayed skeletal ossification, as well as marked chondronecrosis of articular, auricular, and tracheal cartilages. Phenotypically, the mice thus replicated a number of the pathological features of Kashin-Beck disease, supporting the notion that selenium deficiency is important to the development of this syndrome.

  4. Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins.

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    Donovan, Jesse; Copeland, Paul R

    2009-09-10

    The co-translational incorporation of selenocysteine into nascent polypeptides by recoding the UGA stop codon occurs in all domains of life. In eukaryotes, this event requires at least three specific factors: SECIS binding protein 2 (SBP2), a specific translation elongation factor (eEFSec), selenocysteinyl tRNA, and a cis-acting selenocysteine insertion sequence (SECIS) element in selenoprotein mRNAs. While the phylogenetic relationships of selenoprotein families and the evolution of selenocysteine usage are well documented, the evolutionary history of SECIS binding proteins has not been explored. In this report we present a phylogeny of the eukaryotic SECIS binding protein family which includes SBP2 and a related protein we herein term SBP2L. Here we show that SBP2L is an SBP2 paralogue in vertebrates and is the only form of SECIS binding protein in invertebrate deuterostomes, suggesting a key role in Sec incorporation in these organisms, but an SBP2/SBP2L fusion protein is unable to support Sec incorporation in vitro. An in-depth phylogenetic analysis of the conserved L7Ae RNA binding domain suggests an ancestral relationship with ribosomal protein L30. In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5. Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages. In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.

  5. The Human SepSecS-tRNA[superscript Sec] Complex Reveals the Mechanism of Selenocysteine Formation

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    Palioura, Sotiria; Sherrer, R. Lynn; Steitz, Thomas A.; Söll, Dieter; Simonovic, Miljan; (Yale); (UIC)

    2009-08-13

    Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNA{sup Sec} in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate-dependent mechanism of Sec-tRNA{sup Sec} formation. Two tRNA{sup Sec} molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13-base pair acceptor-T{Upsilon}C arm (where {Upsilon} indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA{sup Sec}, but not free phosphoserine, to be oriented properly for the reaction to occur.

  6. Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing.

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    Strub, Marie Paule; Hoh, François; Sanchez, Jean Frédéric; Strub, Jean Marc; Böck, August; Aumelas, André; Dumas, Christian

    2003-11-01

    A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.

  7. Compositions and methods for making selenocysteine containing polypeptides

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    Soll, Dieter; Aldag, Caroline; Hohn, Michael

    2016-10-11

    Non-naturally occurring tRNA.sup.Sec and methods of using them for recombinant expression of proteins engineered to include one or more selenocysteine residues are disclosed. The non-naturally occurring tRNA.sup.Sec can be used for recombinant manufacture of selenocysteine containing polypeptides encoded by mRNA without the requirement of an SECIS element. In some embodiments, selenocysteine containing polypeptides are manufactured by co-expressing a non-naturally occurring tRNA.sup.Sec a recombinant expression system, such as E. coli, with SerRS, EF-Tu, SelA, or PSTK and SepSecS, and an mRNA with at least one codon that recognizes the anticodon of the non-naturally occurring tRNA.sup.Sec.

  8. Shaping tRNA

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    Priano, Christine

    2013-01-01

    This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

  9. Selenocysteine biosynthesis and insertion machinery in Naegleria gruberi.

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    da Silva, M T A; Caldas, V E A; Costa, F C; Silvestre, D A M M; Thiemann, O H

    2013-04-01

    Selenium (Se) is an essential trace element primarily found in selenoproteins as the 21st amino acid (selenocysteine, Sec, or U). Selenoproteins play an important role in growth and proliferation and are typically involved in cellular redox balance. Selenocysteine is encoded by an in-frame UGA codon specified by a stem-loop structure, the Sec insertion sequence element (SECIS), which, in eukaryotes, is located in the 3'-untranslated region (UTR). The availability of the Naegleria gruberi (ATCC 30224) genome sequence and the use of this organism as a model system for the pathogenic amoeba N. fowleri allowed us to investigate the Sec incorporation pathway in this primitive eukaryote. Using bioinformatics tools, we identified gene sequences encoding PSTK (O-phosphoseryl-tRNA(Sec) kinase), SepSecS (O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase), SelD/SPS2 (selenophosphate synthetase), EFSec (selenocysteine-specific elongation factor) and SBP (SECIS binding protein). These findings were confirmed by RT-PCR and by sequencing. A potential tRNA(Ser)Sec (SelC) gene and a putative selenoprotein with sequence similarity to a mitochondrial thioredoxin reductase (TR3) were also identified. Our results show that the selenocysteine incorporation machinery is indeed present in N. gruberi. Interestingly, the SelD/SPS2 gene is 2214 bp in length and contains two distinct domains. The N-terminal region shows sequence similarity to predicted methyltransferase proteins, and the C-terminal region is homologous to prokaryotic SelD/SPS2. Our results suggest the possibility of novel selenoproteins.

  10. Co2+ binding cysteine and selenocysteine: a DFT study.

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    Spezia, Riccardo; Tournois, Guewen; Cartailler, Thierry; Tortajada, Jeanine; Jeanvoine, Yannick

    2006-08-10

    In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species. In particular, we have focused our attention on the role of sulfur and selenium in the metal binding process and on the resulting deprotonation of the thiol and seleniol functions. From the present calculations we are able to explain, both from electronic structure and thermochemical point of views, a metal-induced thiol deprotonation as observed in gas-phase experiments. A similar process is expected in the case of selenocysteine. In fact, cobalt was found to have a preferential affinity with respect to thiolate and selenolate functions. This can be related to the observation that only S and Se are able-in thiolate and selenolate states-to make a partial charge transfer to the cobalt thus forming very stable complexes. Globally, very similar results are found when substituting S with Se, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets.

  11. Selenocysteine in thiol/disulfide-like exchange reactions.

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    Hondal, Robert J; Marino, Stefano M; Gladyshev, Vadim N

    2013-05-01

    Among trace elements used as cofactors in enzymes, selenium is unique in that it is incorporated into proteins co-translationally in the form of an amino acid, selenocysteine (Sec). Sec differs from cysteine (Cys) by only one atom (selenium versus sulfur), yet this switch dramatically influences important aspects of enzyme reactivity. The main focus of this review is an updated and critical discussion on how Sec might be used to accelerate thiol/disulfide-like exchange reactions in natural selenoenzymes, compared with their Cys-containing homologs. We discuss in detail three major aspects associated with thiol/disulfide exchange reactions: (i) nucleophilicity of the attacking thiolate (or selenolate); (ii) electrophilicity of the center sulfur (or selenium) atom; and (iii) stability of the leaving group (sulfur or selenium). In all these cases, we analyze the benefits that selenium might provide in these types of reactions. It is the biological thiol oxidoreductase-like function that benefits from the use of Sec, since Sec functions to chemically accelerate the rate of these reactions. We review various hypotheses that could help explain why Sec is used in enzymes, particularly with regard to competitive chemical advantages provided by the presence of the selenium atom in enzymes. Ultimately, these chemical advantages must be connected to biological functions of Sec.

  12. Network of tRNA Gene Sequences

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    WEI Fang-ping; LI Sheng; MA Hong-ru

    2008-01-01

    A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distribution to scale-free distribution when the similarity degree of the tRNA gene sequences increases. The tRNA gene sequences with the same anticodon identity are more self-organized than those with different anticodon identities and form local clusters in the network. Some vertices of the local cluster have a high connection with other local clusters, and the probable reason was given. Moreover, a network constructed by the same number of random tRNA sequences was used to make comparisons. The relationships between the properties of the tRNA similarity network and the characters of tRNA evolutionary history were discussed.

  13. Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

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    Kim, Moon-Jung [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of); Lee, Byung Cheon [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Hwang, Kwang Yeon [Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Gladyshev, Vadim N. [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Kim, Hwa-Young, E-mail: hykim@ynu.ac.kr [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of)

    2015-06-12

    Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. {sup 75}Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher K{sub m} than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec. - Highlights: • The first characterization of a selenoprotein Trx is presented. • The selenoenzyme Trx exhibits 10-fold higher catalytic activity than Cys homologues. • Se utilization in Trx is primarily due to the catalytic advantage provided by Sec residue.

  14. Methylated nucleosides in tRNA and tRNA methyltransferases

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    Hiroyuki eHori

    2014-05-01

    Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

  15. Is tRNA binding or tRNA mimicry mandatory for translation factors?

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    Kristensen, Ole; Laurberg, Martin; Liljas, Anders; Selmer, Maria

    2002-02-01

    tRNA is the adaptor in the translation process. The ribosome has three sites for tRNA, the A-, P-, and E-sites. The tRNAs bridge between the ribosomal subunits with the decoding site and the mRNA on the small or 30S subunit and the peptidyl transfer site on the large or 50S subunit. The possibility that translation release factors could mimic tRNA has been discussed for a long time, since their function is very similar to that of tRNA. They identify stop codons of the mRNA presented in the decoding site and hydrolyse the nascent peptide from the peptidyl tRNA in the peptidyl transfer site. The structures of eubacterial release factors are not yet known, and the first example of tRNA mimicry was discovered when elongation factor G (EF-G) was found to have a closely similar shape to a complex of elongation factor Tu (EF-Tu) with aminoacyl-tRNA. An even closer imitation of the tRNA shape is seen in ribosome recycling factor (RRF). The number of proteins mimicking tRNA is rapidly increasing. This primarily concerns translation factors. It is now evident that in some sense they are either tRNA mimics, GTPases or possibly both.

  16. Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.

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    Jiang, Yongying; Trnka, Michael J; Medzihradszky, Katalin F; Ouellet, Hugues; Wang, Yongqiang; Ortiz de Montellano, Paul R

    2009-03-01

    To characterize heme oxygenase with a selenocysteine (SeCys) as the proximal iron ligand, we have expressed truncated human heme oxygenase-1 (hHO-1) His25Cys, in which Cys-25 is the only cysteine, in the Escherichia coli cysteine auxotroph strain BL21(DE3)cys. Selenocysteine incorporation into the protein was demonstrated by both intact protein mass measurement and mass spectrometric identification of the selenocysteine-containing tryptic peptide. One selenocysteine was incorporated into approximately 95% of the expressed protein. Formation of an adduct with Ellman's reagent (DTNB) indicated that the selenocysteine in the expressed protein was in the reduced state. The heme-His25SeCys hHO-1 complex could be prepared by either (a) supplementing the overexpression medium with heme, or (b) reconstituting the purified apoprotein with heme. Under reducing conditions in the presence of imidazole, a covalent bond is formed by addition of the selenocysteine residue to one of the heme vinyl groups. No covalent bond is formed when the heme is replaced by mesoheme, in which the vinyls are replaced by ethyl groups. These results, together with our earlier demonstration that external selenolate ligands can transfer an electron to the iron [Y. Jiang, P.R. Ortiz de Montellano, Inorg. Chem. 47 (2008) 3480-3482 ], indicate that a selenyl radical is formed in the hHO-1 His25SeCys mutant that adds to a heme vinyl group.

  17. Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.

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    Palioura, Sotiria; Herkel, Johannes; Simonović, Miljan; Lohse, Ansgar W; Söll, Dieter

    2010-07-01

    Selenocysteine, the 21st genetically encoded amino acid, is the major form of the antioxidant trace element selenium in the human body. In eukaryotes and archaea its synthesis proceeds through a phosphorylated intermediate in a tRNA-dependent fashion. The final step of selenocysteine formation is catalyzed by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) that converts phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec). The human SepSecS protein is also known as soluble liver antigen/liver pancreas (SLA/LP), which represents one of the antigens of autoimmune hepatitis. Here we review the discovery of human SepSecS and the current understanding of the immunogenicity of SLA/LP in autoimmune hepatitis.

  18. Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA

    DEFF Research Database (Denmark)

    Leihne, Vibeke; Kirpekar, Finn; Vågbø, Cathrine B

    2011-01-01

    demonstrate, both by in vitro and in vivo studies, that the Arabidopsis thaliana methyltransferase AT1G31600, denoted by us AtTRM9, is responsible for the final step in mcm(5)U formation, thus representing a functional homologue of the Saccharomyces cerevisiae Trm9 protein. We also show that the enzymatic......(5)U- and mcm(5)Um-containing forms of the selenocysteine-specific tRNA(Sec) in mammals reflects an important regulatory process. The present study reveals a role in for several hitherto uncharacterized Arabidopsis proteins in the formation of modified wobble uridines.......Uridine at the wobble position of tRNA is usually modified, and modification is required for accurate and efficient protein translation. In eukaryotes, wobble uridines are modified into 5-methoxycarbonylmethyluridine (mcm(5)U), 5-carbamoylmethyluridine (ncm(5)U) or derivatives thereof. Here, we...

  19. tRNA Biology in Mitochondria

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    Thalia Salinas-Giegé

    2015-02-01

    Full Text Available Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.

  20. tRNA Biology in Mitochondria

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    Salinas-Giegé, Thalia; Giegé, Richard; Giegé, Philippe

    2015-01-01

    Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation. PMID:25734984

  1. Split Quasi-adequate Semigroups

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    Xiao Jiang GUO; Ting Ting PENG

    2012-01-01

    The so-called split IC quasi-adequate semigroups are in the class of idempotent-connected quasi-adequate semigroups.It is proved that an IC quasi-adequate semigroup is split if and only if it has an adequate transversal.The structure of such semigroup whose band of idempotents is regular will be particularly investigated.Our obtained results enrich those results given by McAlister and Blyth on split orthodox semigroups.

  2. Species-specific identity elements of tRNA Trp

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Through the comparisons among 91 tRNA Trp sequences from prokaryotes, archea and eukaryotes, the potential species-specific identity elements of tRNA Trp are found to be located within acceptor stem, dihydrouridine (D) stem, anticodon(AC) stem and discriminator base. Mutagenesis of B. subtilis tRNA Trp to the eukaryotic consensus se quence, in vitro transcription and enzymatic assay of tRNA Trp toward different tryptophanyl-tRNA synthetases (TrpRS) were employed to shed light on these species-specific identity elements and demonstrate the accurate recognition and the coevolution between tRNA and TrpRS. B. subtilis tRNA Trp with its acceptor stem and discriminator base transplanted by eukaryotic counterparts exhibited diminished reactivity toward B. subtilis enzyme but could be efficiently aminoacylated by rat liver crude enzyme. In contrast, B. subtilis tRNA Trp analog with the eukaryotic anticodon stem and D stem retains its recognition by B. subtilis enzyme. The results provide a strong evidence that the species-specific identity elements of tRNA Trp are orientated within the acceptor stem and discriminator base of tRNA Trp, and the anticodon stem and D stem are of little importance to the interaction between tRNA Trp and its cognate synthetase (TrpRS).

  3. Compilation of tRNA sequences.

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    Sprinzl, M; Grueter, F; Spelzhaus, A; Gauss, D H

    1980-01-11

    This compilation presents in a small space the tRNA sequences so far published. The numbering of tRNAPhe from yeast is used following the rules proposed by the participants of the Cold Spring Harbor Meeting on tRNA 1978 (1,2;Fig. 1). This numbering allows comparisons with the three dimensional structure of tRNAPhe. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguosly analyzed. Rare nucleosides are named according to the IUPACIUB rules (for complicated rare nucleosides and their identification see Table 1); those with lengthy names are given with the prefix x and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information the reader is referred either to the original literature or to other tRNA sequence compilations (3-7). Mutant tRNAs are dealt with in a compilation by J. Celis (8). The compilers would welcome any information by the readers regarding missing material or erroneous presentation. On the basis of this numbering system computer printed compilations of tRNA sequences in a linear form and in cloverleaf form are in preparation.

  4. Kinetic Analysis of tRNA Methylfransferases

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    Hou, Ya-Ming; Masuda, Isao

    2016-01-01

    Transfer RNA (tRNA) molecules contain many chemical modifications that are introduced after transcription. A major form of these modifications is methyl transfer to bases and backbone groups, using S-adenosyl methionine (AdoMet) as the methyl donor. Each methylation confers a specific advantage to tRNA in structure or in function. A remarkable methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA, which suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. This chapter summarizes the kinetic assays that are used to reveal the distinction between TrmD and Trm5. Three types of assays are described, the steady-state, the pre-steady-state, and the single turnover assays, which collectively provide the basis for mechanistic investigation of AdoMet-dependent methyl transfer reactions. PMID:26253967

  5. RNA versatility governs tRNA function: Why tRNA flexibility is essential beyond the translation cycle.

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    Kuhn, Claus-D

    2016-05-01

    tRNAs undergo multiple conformational changes during the translation cycle that are required for tRNA translocation and proper communication between the ribosome and translation factors. Recent structural data on how destabilized tRNAs utilize the CCA-adding enzyme to proofread themselves put a spotlight on tRNA flexibility beyond the translation cycle. In analogy to tRNA surveillance, this review finds that other processes also exploit versatile tRNA folding to achieve, amongst others, specific aminoacylation, translational regulation by riboswitches or a block of bacterial translation. tRNA flexibility is thereby not restricted to the hinges utilized during translation. In contrast, the flexibility of tRNA is distributed all over its L-shape and is actively exploited by the tRNA-interacting partners to discriminate one tRNA from another. Since the majority of tRNA modifications also modulate tRNA flexibility it seems that cells devote enormous resources to tightly sense and regulate tRNA structure. This is likely required for error-free protein synthesis.

  6. Hyperbolic semi-adequate links

    OpenAIRE

    Futer, David; Kalfagianni, Efstratia; Purcell, Jessica S.

    2013-01-01

    We provide a diagrammatic criterion for semi-adequate links to be hyperbolic. We also give a conjectural description of the satellite structures of semi-adequate links. One application of our result is that the closures of sufficiently complicated positive braids are hyperbolic links.

  7. HUMAN MITOCHONDRIAL tRNA MUTATIONS IN MATERNALLY INHERITED DEAFNESS

    Institute of Scientific and Technical Information of China (English)

    ZHENG Jing; GONG Sha-sha; TANG Xiao-wen; ZHU Yi; GUAN Min-xin

    2013-01-01

    Mutations in mitochondrial tRNA genes have been shown to be associated with maternally inherited syn-dromic and non-syndromic deafness. Among those, mutations such as tRNALeu(UUR) 3243A>G associated with syndromic deafness are often present in heteroplasmy, and the non-syndromic deafness-associated tRNA mu-tations including tRNASer(UCN) 7445A>G are often in homoplasmy or in high levels of heteroplasmy. These tRNA mutations are the primary factors underlying the development of hearing loss. However, other tRNA mutations such as tRNAThr 15927G>A and tRNASer(UCN) 7444G>A are insufficient to produce a deafness phe-notype, but always act in synergy with the primary mitochondrial DNA mutations, and can modulate their phenotypic manifestation. These tRNA mutations may alter the structure and function of the corresponding mitochondrial tRNAs and cause failures in tRNAs metabolism. Thereby, the impairment of mitochondrial protein synthesis and subsequent defects in respiration caused by these tRNA mutations, results in mitochon-drial dysfunctions and eventually leads to the development of hearing loss. Here, we summarized the deaf-ness-associated mitochondrial tRNA mutations and discussed the pathophysiology of these mitochondrial tRNA mutations, and we hope these data will provide a foundation for the early diagnosis, management, and treatment of maternally inherited deafness.

  8. [cDNA cloning, expression and determination of substrate specificity of mice selenocysteine-containing protein SelV (Selenoprotein V)].

    Science.gov (United States)

    Varlamova, E G; Novoselov, S V; Novoselov, V I

    2015-01-01

    To date various bioinformatics tools allowed to identify 25 selenocysteine-containing mammalian proteins. The name of these proteins assumes that they contain the amino acid selenocysteine (Sec). Functionally characterized selenocysteine-containing proteins are oxidoreductases with various functions, including glutathione peroxidases, thioredoxin reductases, deiodinases etc. However, the functions of more than half of identified proteins are still unclear, and mammalian selenoprotein SeIV is among them. We studied the selV in all stages of postnatal development with the maximum level of mRNA expression during puberty, whereas in adult mice (8-18 months) we observed a gradual decrease of expression. In order to get closer to the functional role of Selenoprotein V, we have carried out experiments on the substrate specificity and enzymatic activity measurement of this selenocysteine-containing protein. It was shown that SelV posseses glutathionperoxidase and thioredoxinreductase activities.

  9. Diversity in mechanism and function of tRNA methyltransferases

    Science.gov (United States)

    Swinehart, William E; Jackman, Jane E

    2015-01-01

    tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed. PMID:25626150

  10. tRNA - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us RMG tRNA... Data detail Data name tRNA DOI 10.18908/lsdba.nbdc00193-006 Description of data con...tents Data contents are as follows: Amino acid sequences of 23 tRNA from 17 species identified in the rice m...n Amino acids Amino acid binding to tRNA tRNA tRNA gene indicated by the cognate amino acid in one-letter code rice Rice +: tRNA... present -: tRNA absent y: pseudogene a: mitochondrial tRNA b: plastid-like tRNA Miyata

  11. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability.

    Science.gov (United States)

    Copela, Laura A; Chakshusmathi, Ghadiyaram; Sherrer, R Lynn; Wolin, Sandra L

    2006-04-01

    Although the La protein stabilizes nascent pre-tRNAs from nucleases, influences the pathway of pre-tRNA maturation, and assists correct folding of certain pre-tRNAs, it is dispensable for growth in both budding and fission yeast. Here we show that the Saccharomyces cerevisiae La shares functional redundancy with both tRNA modification enzymes and other proteins that contact tRNAs during their biogenesis. La is important for growth in the presence of mutations in either the arginyl tRNA synthetase or the tRNA modification enzyme Trm1p. In addition, two pseudouridine synthases, PUS3 and PUS4, are important for growth in strains carrying a mutation in tRNA(Arg)(CCG) and are essential when La is deleted in these strains. Depletion of Pus3p results in accumulation of the aminoacylated mutant tRNA(Arg)(CCG) in nuclei, while depletion of Pus4p results in decreased stability of the mutant tRNA. Interestingly, the degradation of mutant unstable forms of tRNA(Arg)(CCG) does not require the Trf4p poly(A) polymerase, suggesting that yeast cells possess multiple pathways for tRNA decay. These data demonstrate that La functions redundantly with both tRNA modifications and proteins that associate with tRNAs to achieve tRNA structural stability and efficient biogenesis.

  12. Kinetic and mutational studies of three NifS homologs from Escherichia coli: mechanistic difference between L-cysteine desulfurase and L-selenocysteine lyase reactions.

    Science.gov (United States)

    Mihara, H; Kurihara, T; Yoshimura, T; Esaki, N

    2000-04-01

    We have purified three NifS homologs from Escherichia coli, CSD, CsdB, and IscS, that appear to be involved in iron-sulfur cluster formation and/or the biosynthesis of selenophosphate. All three homologs catalyze the elimination of Se and S from L-selenocysteine and L-cysteine, respectively, to form L-alanine. These pyridoxal 5'-phosphate enzymes were inactivated by abortive transamination, yielding pyruvate and a pyridoxamine 5'-phosphate form of the enzyme. The enzymes showed non-Michaelis-Menten behavior for L-selenocysteine and L-cysteine. When pyruvate was added, they showed Michaelis-Menten behavior for L-selenocysteine but not for L-cysteine. Pyruvate significantly enhanced the activity of CSD toward L-selenocysteine. Surprisingly, the enzyme activity toward L-cysteine was not increased as much by pyruvate, suggesting the presence of different rate-limiting steps or reaction mechanisms for L-cysteine desulfurization and the degradation of L-selenocysteine. We substituted Ala for each of Cys358 in CSD, Cys364 in CsdB, and Cys328 in IscS, residues that correspond to the catalytically essential Cys325 of Azotobacter vinelandii NifS. The enzyme activity toward L-cysteine was almost completely abolished by the mutations, whereas the activity toward L-selenocysteine was much less affected. This indicates that the reaction mechanism of L-cysteine desulfurization is different from that of L-selenocysteine decomposition, and that the conserved cysteine residues play a critical role only in L-cysteine desulfurization.

  13. Kinetic consequences of introducing a proximal selenocysteine ligand into cytochrome P450cam.

    Science.gov (United States)

    Vandemeulebroucke, An; Aldag, Caroline; Stiebritz, Martin T; Reiher, Markus; Hilvert, Donald

    2015-11-10

    The structural, electronic, and catalytic properties of cytochrome P450cam are subtly altered when the cysteine that coordinates to the heme iron is replaced with a selenocysteine. To map the effects of the sulfur-to-selenium substitution on the individual steps of the catalytic cycle, we conducted a comparative kinetic analysis of the selenoenzyme and its cysteine counterpart. Our results show that the more electron-donating selenolate ligand has only negligible effects on substrate, product, and oxygen binding, electron transfer, catalytic turnover, and coupling efficiency. Off-pathway reduction of oxygen to give superoxide is the only step significantly affected by the mutation. Incorporation of selenium accelerates this uncoupling reaction approximately 50-fold compared to sulfur, but because the second electron transfer step is much faster, the impact on overall catalytic turnover is minimal. Density functional theory calculations with pure and hybrid functionals suggest that superoxide formation is governed by a delicate interplay of spin distribution, spin state, and structural effects. In light of the remarkably similar electronic structures and energies calculated for the sulfur- and selenium-containing enzymes, the ability of the heavier atom to enhance the rate of spin crossover may account for the experimental observations. Because the selenoenzyme closely mimics wild-type P450cam, even at the level of individual steps in the reaction cycle, selenium represents a unique mechanistic probe for analyzing the role of the proximal ligand and spin crossovers in P450 chemistry.

  14. Systematic Comparisons of Orthologous Selenocysteine Methyltransferase and Homocysteine Methyltransferase Genes from Seven Monocots Species

    Directory of Open Access Journals (Sweden)

    De-yong ZHAO

    2015-06-01

    Full Text Available Identifying and manipulating genes underlying selenium metabolism could be helpful for increasing selenium content in crop grain, which is an important way to overcome diseases resulted from selenium deficiency. A reciprocal smallest distance algorithm (RSD approach was applied using two experimentally confirmed Homocysteine S-Methyltransferases genes (HMT1 and HMT2 and a putative Selenocysteine Methyltransferase (SMT from dicots plant Arabidopsis thaliana, to explore their orthologs in seven sequenced diploid monocot species: Oryza sativa, Zea mays, Sorghum bicolor, Brachypodium distachyon, Hordeum vulgare, Aegilops tauschii (the D-genome donor of common wheat and Triticum urartu (the A-genome donor of common wheat. HMT1 was apparently diverged from HMT2 and most of SMT orthologs were the same with that of HMT2 in this study, leading to the hypothesis that SMT and HMT originate from one common ancestor gene. Identifying orthologs provide candidates for further experimental confirmation; also it could be helpful in designing primers to clone SMT or HMT orthologs in other crops.

  15. Reverse Translocation of tRNA in the Ribosome

    OpenAIRE

    2006-01-01

    A widely held view is that directional movement of tRNA in the ribosome is determined by an intrinsic mechanism and driven thermodynamically by transpeptidation. Here, we show that, in certain ribosomal complexes, the pretranslocation (PRE) state is thermodynamically favored over the posttranslocation (POST) state. Spontaneous and efficient conversion from the POST to PRE state is observed when EF-G is depleted from ribosomes in the POST state or when tRNA is added to the E site of ribosomes ...

  16. tRNA nucleotide 47: an evolutionary enigma.

    Science.gov (United States)

    Cermakian, N; McClain, W H; Cedergren, R

    1998-08-01

    A previous analysis of tRNA sequences suggested a correlation between the absence of a nucleotide at position 47 (nt 47) in the extra loop and the presence of a U13:G22 base pair in the D-stem. We have evaluated the significance of this correlation by determining the in vivo activity of tRNAs containing either a C13:G22 or a U13:G22 pair in tRNA molecules with or without nt 47. Although this correlation might reflect some malfunction of tRNAs lacking nt 47, but containing the C13:G22, assays of the in vivo suppressor activity showed that this tRNA is actually more active than the tRNA with the features found in the database, i.e., a U13:G22 base pair and no nt 47. Moreover, analogous constructs with a GGC anticodon permitted the growth of an Escherichia coli strain deleted for tRNA(Ala)GGC genes equally well. On the other hand, long-term growth experiments with competing E. coli strains harboring the tRNA lacking nt 47, either with the C13:G22 or the U13:G22 base pair demonstrated that the U13:G22 tRNA overtook the C13:G22 strain even when the starting proportion of strains favored the C13:G22 strain. Thus, the preference for the U13:G22 tRNA lacking nt 47 in the sequence database is most likely due to factors that come into play during extended growth or latency rather than to the ability of the tRNA to engage in protein synthesis.

  17. Origins and Early Evolution of the tRNA Molecule

    Directory of Open Access Journals (Sweden)

    Koji Tamura

    2015-12-01

    Full Text Available Modern transfer RNAs (tRNAs are composed of ~76 nucleotides and play an important role as “adaptor” molecules that mediate the translation of information from messenger RNAs (mRNAs. Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3′ terminus of tRNA is also a typical characteristic of the molecule. “Why CCA?” is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC. The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome.

  18. Amino acid modifications on tRNA

    Institute of Scientific and Technical Information of China (English)

    Jing Yuan; Kelly Sheppard; Dieter S(o)ll

    2008-01-01

    The accurate formation of cognate aminoacyl-transfer RNAs (aa-tRNAs) is essential for the fidelity of translation.Most amino acids are esterified onto their cognate tRNA isoacceptors directly by aa.tRNA synthetases.However,in the case of four amino acids (Gin,Asn,Cys and Sec),aminoacyl-tRNAs are made through indirect pathways in many organisms across all three domains of life.The process begins with the charging ofnoncognate amino acids to tRNAs by a specialized synthetase in the case of Cys-tRNAcys formation or by synthetases with relaxed specificity,such as the non-discriminating glutamyl-tRNA,non-discriminating aspartyl-tRNA and seryl-tRNA synthetases.The resulting misacylated tRNAs are then converted to cognate pairs through transformation of the amino acids on the tRNA,which is catalyzed by a group of tRNA-dependent modifying enzymes,such as tRNA-dependent amidotransferases,Sep-tRNA:Cys-tRNA synthase,O-phosphoseryi-tRNA kinase and Sep-tRNA:Sec-tRNA synthase.The majority of these indirect pathways are widely spread in all domains of life and thought to be part of the evolutionary process.

  19. Conformational preferences and pK(a) value of selenocysteine residue.

    Science.gov (United States)

    Byun, Byung Jin; Kang, Young Kee

    2011-05-01

    The conformational preferences of the L-selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac-Sec-NHMe and Ac-Sec(-) -NHMe, respectively) and the apparent (i.e., macroscopic) pK(a) value of the Sec residue have been studied using the dispersion-corrected density functionals M06-2X and B2PLYP-D with the implicit solvation method in the gas phase and in water. In the gas phase, the backbone-to-backbone and/or side chain-to-backbone hydrogen bonds are found to contribute in stabilizing the most preferred conformations for the Sec and Sec(-) residues, as seen for the Cys and Cys(-) residues. However, the polyproline II-like conformations prevail over the conformations with the backbone-to-backbone hydrogen bonds in water because of the weakened hydrogen bonds by the favorable direct interactions between the backbone CO and HN groups and water molecules. The Sec and Sec(-) residues are found to adopt more various conformations than the Cys and Cys(-) residues in water, although the most preferred conformations of the neutral and/or anionic forms of the two residues are similar each other in the gas phase and in water. Using the statistically weighted free energies of the Sec and Sec(-) dipeptides in the gas phase and their solvation free energies, the pK(a) value of the Sec residue is estimated to be 5.47 at 25°C, which is in good agreement with the experimental value of 5.43 ± 0.02. It is found that the lower pK(a) value of the selenol side chain for the Sec residue by ∼3 units than the thiol side chain for the Cys residue is ascribed to the higher gas-phase acidity of the Sec residue. Copyright © 2011 Wiley Periodicals, Inc.

  20. Reverse translocation of tRNA in the ribosome.

    Science.gov (United States)

    Shoji, Shinichiro; Walker, Sarah E; Fredrick, Kurt

    2006-12-28

    A widely held view is that directional movement of tRNA in the ribosome is determined by an intrinsic mechanism and driven thermodynamically by transpeptidation. Here, we show that, in certain ribosomal complexes, the pretranslocation (PRE) state is thermodynamically favored over the posttranslocation (POST) state. Spontaneous and efficient conversion from the POST to PRE state is observed when EF-G is depleted from ribosomes in the POST state or when tRNA is added to the E site of ribosomes containing P-site tRNA. In the latter assay, the rate of tRNA movement is increased by streptomycin and neomycin, decreased by tetracycline, and not affected by the acylation state of the tRNA. In one case, we provide evidence that complex conversion occurs by reverse translocation (i.e., direct movement of the tRNAs from the E and P sites to the P and A sites, respectively). These findings have important implications for the energetics of translocation.

  1. The tRNA Elbow in Structure, Recognition and Evolution

    Directory of Open Access Journals (Sweden)

    Jinwei Zhang

    2016-01-01

    Full Text Available Prominent in the L-shaped three-dimensional structure of tRNAs is the “elbow” where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow.

  2. Biochemical discrimination between selenium and sulfur 2: mechanistic investigation of the selenium specificity of human selenocysteine lyase.

    Directory of Open Access Journals (Sweden)

    Ann-Louise Johansson

    Full Text Available Selenium is an essential trace element incorporated into selenoproteins as selenocysteine. Selenocysteine (Sec lyases (SCLs and cysteine (Cys desulfurases (CDs catalyze the removal of selenium or sulfur from Sec or Cys, respectively, and generally accept both substrates. Intriguingly, human SCL (hSCL is specific for Sec even though the only difference between Sec and Cys is a single chalcogen atom.The crystal structure of hSCL was recently determined and gain-of-function protein variants that also could accept Cys as substrate were identified. To obtain mechanistic insight into the chemical basis for its substrate discrimination, we here report time-resolved spectroscopic studies comparing the reactions of the Sec-specific wild-type hSCL and the gain-of-function D146K/H389T variant, when given Cys as a substrate. The data are interpreted in light of other studies of SCL/CD enzymes and offer mechanistic insight into the function of the wild-type enzyme. Based on these results and previously available data we propose a reaction mechanism whereby the Sec over Cys specificity is achieved using a combination of chemical and physico-mechanical control mechanisms.

  3. Biochemical discrimination between selenium and sulfur 2: mechanistic investigation of the selenium specificity of human selenocysteine lyase.

    Science.gov (United States)

    Johansson, Ann-Louise; Collins, Ruairi; Arnér, Elias S J; Brzezinski, Peter; Högbom, Martin

    2012-01-01

    Selenium is an essential trace element incorporated into selenoproteins as selenocysteine. Selenocysteine (Sec) lyases (SCLs) and cysteine (Cys) desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys, respectively, and generally accept both substrates. Intriguingly, human SCL (hSCL) is specific for Sec even though the only difference between Sec and Cys is a single chalcogen atom.The crystal structure of hSCL was recently determined and gain-of-function protein variants that also could accept Cys as substrate were identified. To obtain mechanistic insight into the chemical basis for its substrate discrimination, we here report time-resolved spectroscopic studies comparing the reactions of the Sec-specific wild-type hSCL and the gain-of-function D146K/H389T variant, when given Cys as a substrate. The data are interpreted in light of other studies of SCL/CD enzymes and offer mechanistic insight into the function of the wild-type enzyme. Based on these results and previously available data we propose a reaction mechanism whereby the Sec over Cys specificity is achieved using a combination of chemical and physico-mechanical control mechanisms.

  4. Selenol protecting groups in organic chemistry: special emphasis on selenocysteine Se-protection in solid phase peptide synthesis.

    Science.gov (United States)

    Flemer, Stevenson

    2011-04-18

    The appearance of selenium in organic synthesis is relatively rare, and thus examples in the literature pertaining to the masking of its considerable reactivity are similarly uncommon. Greene's Protecting Groups in Organic Synthesis, the standard reference for the state of the art in this arena, offers no entries for selenium protective methodology, in stark comparison to its mention of the great variety of protecting groups germane to its chalcogen cousin sulfur. This scarcity of Se-protection methods makes it no less interesting and pertinent toward the construction of selenium-containing organic systems which do indeed require the iterative blocking and de-blocking of selenol functionalities. A selenium-containing system which is especially relevant is selenocysteine, as its use in Solid Phase Peptide Synthesis requires extensive protection of its selenol side chain. This review will attempt to summarize the current state of understanding with regard to selenium protection protocol in organic synthesis. Moreover, it will provide a special emphasis on selenocysteine side chain protection, comprising both the breadth of functionality used for this purpose as well as methods of deprotection.

  5. Selenol Protecting Groups in Organic Chemistry: Special Emphasis on Selenocysteine Se-Protection in Solid Phase Peptide Synthesis

    Directory of Open Access Journals (Sweden)

    Stevenson Flemer Jr.

    2011-04-01

    Full Text Available The appearance of selenium in organic synthesis is relatively rare, and thus examples in the literature pertaining to the masking of its considerable reactivity are similarly uncommon. Greene's Protecting Groups in Organic Synthesis, the standard reference for the state of the art in this arena, offers no entries for selenium protective methodology, in stark comparison to its mention of the great variety of protecting groups germane to its chalcogen cousin sulfur. This scarcity of Se-protection methods makes it no less interesting and pertinent toward the construction of selenium-containing organic systems which do indeed require the iterative blocking and de-blocking of selenol functionalities. A selenium-containing system which is especially relevant is selenocysteine, as its use in Solid Phase Peptide Synthesis requires extensive protection of its selenol side chain. This review will attempt to summarize the current state of understanding with regard to selenium protection protocol in organic synthesis. Moreover, it will provide a special emphasis on selenocysteine side chain protection, comprising both the breadth of functionality used for this purpose as well as methods of deprotection.

  6. Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme.

    Science.gov (United States)

    Mihara, H; Kurihara, T; Yoshimura, T; Soda, K; Esaki, N

    1997-09-05

    Selenocysteine lyase (EC 4.4.1.16) exclusively decomposes selenocysteine to alanine and elemental selenium, whereas cysteine desulfurase (NIFS protein) of Azotobacter vinelandii acts indiscriminately on both cysteine and selenocysteine to produce elemental sulfur and selenium respectively, and alanine. These proteins exhibit some sequence homology. The Escherichia coli genome contains three genes with sequence homology to nifS. We have cloned the gene mapped at 63.4 min in the chromosome and have expressed, purified to homogeneity, and characterized the gene product. The enzyme comprises two identical subunits with 401 amino acid residues (Mr 43,238) and contains pyridoxal 5'-phosphate as a coenzyme. The enzyme catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine. Because L-cysteine sulfinic acid was desulfinated to form L-alanine as the preferred substrate, we have named this new enzyme cysteine sulfinate desulfinase. Mutant enzymes having alanine substituted for each of the four cysteinyl residues (Cys-100, Cys-176, Cys-323, and Cys-358) were all active. Cys-358 corresponds to Cys-325 of A. vinelandii NIFS, which is conserved among all NIFS-like proteins and catalytically essential (Zheng, L., White, R. H., Cash, V. L., and Dean, D. R. (1994) Biochemistry 33, 4714-4720), is not required for cysteine sulfinate desulfinase. Thus, the enzyme is distinct from A. vinelandii NIFS in this respect.

  7. Probing tRNA interaction with biogenic polyamines.

    Science.gov (United States)

    Ouameur, Amin Ahmed; Bourassa, Philippe; Tajmir-Riahi, Heidar-Ali

    2010-10-01

    Biogenic polyamines are found to modulate protein synthesis at different levels. This effect may be explained by the ability of polyamines to bind and influence the secondary structure of tRNA, mRNA, and rRNA. We report the interaction between tRNA and the three biogenic polyamines putrescine, spermidine, spermine, and cobalt(III)hexamine at physiological conditions, using FTIR spectroscopy, capillary electrophoresis, and molecular modeling. The results indicated that tRNA was stabilized at low biogenic polyamine concentration, as a consequence of polyamine interaction with the backbone phosphate group. The main tRNA reactive sites for biogenic polyamine at low concentration were guanine-N7/O6, uracil-O2/O4, adenine-N3, and 2'OH of the ribose. At high polyamine concentration, the interaction involves guanine-N7/O6, adenine-N7, uracil-O2 reactive sites, and the backbone phosphate group. The participation of the polycation primary amino group, in the interaction and the presence of the hydrophobic contact, are also shown. The binding affinity of biogenic polyamine to tRNA molecule was in the order of spermine > spermidine > putrescine with K(Spm) = 8.7 × 10(5) M(-1), K(Spd) = 6.1 × 10(5) M(-1), and K(Put) = 1.0 × 10(5) M(-1), which correlates with their positively charged amino group content. Hill analysis showed positive cooperativity for the biogenic polyamines and negative cooperativity for cobalt-hexamine. Cobalt(III)hexamine contains high- and low-affinity sites in tRNA with K(1) = 3.2 × 10(5) M(-1) and K(2) = 1.7 × 10(5) M(-1), that have been attributed to the interactions with guanine-N7 sites and the backbone PO(2) group, respectively. This mechanism of tRNA binding could explain the condensation phenomenon observed at high Co(III) content, as previously shown in the Co(III)-DNA complexes.

  8. 21 CFR 1404.900 - Adequate evidence.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Adequate evidence. 1404.900 Section 1404.900 Food and Drugs OFFICE OF NATIONAL DRUG CONTROL POLICY GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 1404.900 Adequate evidence. Adequate evidence means information sufficient...

  9. Molecular and biochemical characterization of the selenocysteine Se-methyltransferase gene and Se-methylselenocysteine synthesis in broccoli.

    Science.gov (United States)

    Lyi, Sangbom M; Heller, Laurence I; Rutzke, Michael; Welch, Ross M; Kochian, Leon V; Li, Li

    2005-05-01

    Selenium (Se) plays an indispensable role in human nutrition and has been implicated to have important health benefits, including being a cancer preventative agent. While different forms of Se vary in their anticarcinogenic efficacy, Se-methylselenocysteine (SeMSC) has been demonstrated to be one of the most effective chemopreventative compounds. Broccoli (Brassica oleracea var. italica) is known for its ability to accumulate high levels of Se with the majority of the selenoamino acids in the form of Se-methylselenocysteine. Therefore, it serves as a good model to study the regulation of SeMSC accumulation in plants. A cDNA encoding selenocysteine Se-methyltransferase, the key enzyme responsible for SeMSC formation, was cloned from broccoli using a homocysteine S-methyltransferase gene probe from Arabidopsis (Arabidopsis thaliana). This clone, designated as BoSMT, was functionally expressed in Escherichia coli, and its identity was confirmed by its substrate specificity in the methylation of selenocysteine. The BoSMT gene represents a single copy sequence in the broccoli genome. Examination of BoSMT gene expression and SeMSC accumulation in response to selenate, selenite, and sulfate treatments showed that the BoSMT transcript and SeMSC synthesis were significantly up-regulated in plants exposed to selenate but were low in plants supplied with selenite. Simultaneous treatment of selenate with selenite significantly reduced SeMSC production. In addition, high levels of sulfate suppressed selenate uptake, resulting in a dramatic reduction of BoSMT mRNA level and SeMSC accumulation. Our results reveal that SeMSC accumulation closely correlated with the BoSMT gene expression and the total Se status in tissues and provide important information for maximizing the SeMSC production in this beneficial vegetable plant.

  10. Gold nanoparticles combined with highly expressed amber suppressor tRNA: a future antibacterial agent

    Directory of Open Access Journals (Sweden)

    Xiaoda Song

    2010-10-01

    Full Text Available "nAmber suppressor tRNA is a mutant allele coding for a tRNA, whose anticodon is altered in such a way that the suppressor tRNA inserts an amino acid at an amber codon in translation which leads to suppressing (preventing termination. And some Amber suppressor tRNA strains were found. We propose that gold nanoparticles combined with highly expressed amber suppressor tRNA which can be uptake by cells and recognized by AARS (aminoacyl tRNA synthetase will lead to the formation of C-terminally extended proteins. These proteins probably will not work properly, leading bacteria's death. Because of the difference of tRNA between prokaryotic and eukaryotic cells, even between different bacteria species, this amber suppressor tRNA is orthogonal for other species and cannot be recognized by AARS, therefore has no toxicity to other species. May it be an excellent antibacterial agent in the future? In this article we provide a screening method for the highly expressed amber suppressor tRNA using randomly bases mutation, radioactive selection, activity test in vivo, and finally linkage of the amber suppressor tRNA to gold nanoparticles.

  11. A nifS-like gene, csdB, encodes an Escherichia coli counterpart of mammalian selenocysteine lyase. Gene cloning, purification, characterization and preliminary x-ray crystallographic studies.

    Science.gov (United States)

    Mihara, H; Maeda, M; Fujii, T; Kurihara, T; Hata, Y; Esaki, N

    1999-05-21

    Selenocysteine lyase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the exclusive decomposition of L-selenocysteine to L-alanine and elemental selenium. An open reading frame, named csdB, from Escherichia coli encodes a putative protein that is similar to selenocysteine lyase of pig liver and cysteine desulfurase (NifS) of Azotobacter vinelandii. In this study, the csdB gene was cloned and expressed in E. coli cells. The gene product was a homodimer with the subunit Mr of 44,439, contained 1 mol of PLP as a cofactor per mol of subunit, and catalyzed the release of Se, SO2, and S from L-selenocysteine, L-cysteine sulfinic acid, and L-cysteine, respectively, to yield L-alanine; the reactivity of the substrates decreased in this order. Although the enzyme was not specific for L-selenocysteine, the high specific activity for L-selenocysteine (5.5 units/mg compared with 0.019 units/mg for L-cysteine) supports the view that the enzyme can be regarded as an E. coli counterpart of mammalian selenocysteine lyase. We crystallized CsdB, the csdB gene product, by the hanging drop vapor diffusion method. The crystals were of suitable quality for x-ray crystallography and belonged to the tetragonal space group P43212 with unit cell dimensions of a = b = 128.1 A and c = 137.0 A. Consideration of the Matthews parameter Vm (3.19 A3/Da) accounts for the presence of a single dimer in the crystallographic asymmetric unit. A native diffraction dataset up to 2.8 A resolution was collected. This is the first crystallographic analysis of a protein of NifS/selenocysteine lyase family.

  12. Biosynthesis and functions of sulfur modifications in tRNA

    Directory of Open Access Journals (Sweden)

    Naoki eShigi

    2014-04-01

    Full Text Available Sulfur is an essential element for a variety of cellular constituents in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, such as the derivatives of 2‑thiouridine (s2U, 4-thiouridine (s4U, 2-thiocytidine (s2C, and 2-methylthioadenosine (ms2A. Earlier studies established the functions of these modifications for accurate and efficient translation, including proper recognition of the codons in mRNA or stabilization of tRNA structure. In many cases, the biosynthesis of these sulfur modifications starts with cysteine desulfurases, which catalyze the generation of persulfide (an activated form of sulfur from cysteine. Many sulfur-carrier proteins are responsible for delivering this activated sulfur to each biosynthesis pathway. Finally, specific modification enzymes activate target tRNAs and then incorporate sulfur atoms. Intriguingly, the biosynthesis of 2-thiouridine in all domains of life is functionally and evolutionarily related to the ubiquitin-like post-translational modification system of cellular proteins in eukaryotes. This review summarizes the recent characterization of the biosynthesis of sulfur modifications in tRNA and the novel roles of this modification in cellular functions in various model organisms, with a special emphasis on 2-thiouridine derivatives. Each biosynthesis pathway of sulfur-containing molecules is mutually modulated via sulfur trafficking, and 2-thiouridine and codon usage bias have been proposed to control the translation of specific genes.

  13. 5 CFR 919.900 - Adequate evidence.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Adequate evidence. 919.900 Section 919.900 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 919.900 Adequate evidence...

  14. Abundant Semigroups with a Multiplicative Adequate Transversal

    Institute of Scientific and Technical Information of China (English)

    GUO Xiao Jiang

    2002-01-01

    The aim of this paper is to investigate abundant semigroups with a multiplicative adequate transversal. Some properties and characterizations for such semigroups are obtained. In particular,we establish the structure of this class of abundant semigroups in terms of left normal bands, right normal bands and adequate semigroups with some simple compatibility conditions. Finally, we apply this structure to some special cases.

  15. Capture, unfolding, and detection of individual tRNA molecules using a nanopore device

    Directory of Open Access Journals (Sweden)

    Andrew M Smith

    2015-06-01

    Full Text Available Transfer RNAs (tRNA are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules as they are pulled through the α-hemolysin (α-HL nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP, which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified E. coli tRNAfMet and tRNALys, we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provides the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device.

  16. CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.

    Science.gov (United States)

    Weitzer, Stefan; Hanada, Toshikatsu; Penninger, Josef M; Martinez, Javier

    2015-01-01

    Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and tRNA metabolism, RNA stability and protein translation have been linked to motor neuron diseases. Our study on a mouse carrying a catalytically inactive version of the RNA kinase CLP1, a component of the tRNA splicing endonuclease complex, revealed a neurological disorder characterized by progressive loss of lower spinal motor neurons. Surprisingly, mutant mice accumulate a novel class of tRNA-derived fragments. In addition, patients with homozygous missense mutations in CLP1 (R140H) were recently identified who suffer from severe motor-sensory defects, cortical dysgenesis and microcephaly, and exhibit alterations in transfer RNA (tRNA) splicing. Here, we review functions of CLP1 in different RNA pathways and provide hypotheses on the role of the tRNA splicing machinery in the generation of tRNA fragments and the molecular links to neurodegenerative disorders. We further immerse the biology of tRNA splicing into topics of (t)RNA metabolism and oxidative stress, putting forward the idea that defects in tRNA processing leading to tRNA fragment accumulation might trigger the development of neurodegenerative diseases.

  17. Analysis of the complement and molecular evolution of tRNA genes in cow

    Directory of Open Access Journals (Sweden)

    Barris Wesley C

    2009-04-01

    Full Text Available Abstract Background Detailed information regarding the number and organization of transfer RNA (tRNA genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale. Results In this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-GlyCCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-GlyGCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes. Conclusion The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a

  18. Removal of the 5-nitro-2-pyridine-sulfenyl protecting group from selenocysteine and cysteine by ascorbolysis.

    Science.gov (United States)

    Ste Marie, Emma J; Ruggles, Erik L; Hondal, Robert J

    2016-09-01

    We previously reported on a method for the facile removal of 4-methoxybenzyl and acetamidomethyl protecting groups from cysteine (Cys) and selenocysteine (Sec) using 2,2'-dithiobis-5-nitropyridine dissolved in trifluoroacetic acid, with or without thioanisole. The use of this reaction mixture removes the protecting group and replaces it with a 2-thio(5-nitropyridyl) (5-Npys) group. This results in either a mixed selenosulfide bond or disulfide bond (depending on the use of Sec or Cys), which can subsequently be reduced by thiolysis. A major disadvantage of thiolysis is that excess thiol must be used to drive the reaction to completion and then removed before using the Cys-containing or Sec-containing peptide in further applications. Here, we report a further advancement of this method as we have found that ascorbate at pH 4.5 and 25 °C will reduce the selenosulfide to the selenol. Ascorbolysis of the mixed disulfide between Cys and 5-Npys is much less efficient but can be accomplished at higher concentrations of ascorbate at pH 7 and 37 °C with extended reaction times. We envision that our improved method will allow for in situ reactions with alkylating agents and electrophiles without the need for further purification, as well as a number of other applications. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  19. Determination of selenomethionine, selenocysteine, and inorganic selenium in eggs by HPLC-inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lipiec, Elzbieta; Siara, Grzegorz [CNRS/UPPA, Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, Pau (France); Warsaw University of Technology, Warsaw (Poland); Bierla, Katarzyna; Ouerdane, Laurent; Szpunar, Joanna [CNRS/UPPA, Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, Pau (France)

    2010-05-15

    A method for the simultaneous determination of selenomethionine (SeMet), selenocysteine (SeCys), and selenite [Se(IV)] in chicken eggs was developed. A sample preparation protocol including defatting, protein denaturation, and carbamidomethylation was optimized in order to achieve complete protein digestion and to avoid SeCys losses. Quantification was carried out by reversed-phase HPLC-inductively coupled plasma mass spectrometry (ICP MS) after quantitative isolation of the selenium-containing fraction by size-exclusion liquid chromatography. The detection limits were 0.06, 0.003, and 0.01 {mu}g g{sup -1} (dry weight) for SeCys, Se(IV) and SeMet, respectively, and the precision was 5-10%. The end products of carbamidomethylation of the different selenium species were identified for the first time by electrospray QTOF MS after custom-designed 2D HPLC purification. Differences in selenium speciation in egg yolk and white were highlighted, the yolk containing more SeCys and the white more SeMet. An insight into selenium bioaccessibility in eggs was obtained by digestion with simulated gastric and gastrointestinal juices and size-exclusion HPLC-ICP MS. (orig.)

  20. Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.

    Directory of Open Access Journals (Sweden)

    Ruairi Collins

    Full Text Available Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec, the selenium analogue of cysteine (Cys. Sec lyases (SCLs and Cys desulfurases (CDs catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism.

  1. tRNA concentration fine tunes protein solubility.

    Science.gov (United States)

    Fedyunin, Ivan; Lehnhardt, Lothar; Böhmer, Nadine; Kaufmann, Paul; Zhang, Gong; Ignatova, Zoya

    2012-09-21

    Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coli increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.

  2. An alanine tRNA gene cluster from Nephila clavipes.

    Science.gov (United States)

    Luciano, E; Candelas, G C

    1996-06-01

    We report the sequence of a 2.3-kb genomic DNA fragment from the orb-web spider, Nephila clavipes (Nc). The fragment contains four regions of high homology to tRNA(Ala). The members of this irregularly spaced cluster of genes are oriented in the same direction and have the same anticodon (GCA), but their sequence differs at several positions. Initiation and termination signals, as well as consensus intragenic promoter sequences characteristic of tRNA genes, have been identified in all genes. tRNA(Ala) are involved in the regulation of the fibroin synthesis in the large ampullate Nc glands.

  3. Antibiotic inhibition of the movement of tRNA substrates through a peptidyl transferase cavity

    DEFF Research Database (Denmark)

    Porse, B T; Rodriguez-Fonseca, C; Leviev, I

    1996-01-01

    The present review attempts to deal with movement of tRNA substrates through the peptidyl transferase centre on the large ribosomal subunit and to explain how this movement is interrupted by antibiotics. It builds on the concept of hybrid tRNA states forming on ribosomes and on the observed movem...

  4. Real Time Investments with Adequate Portfolio Theory

    Directory of Open Access Journals (Sweden)

    Alina Kvietkauskienė

    2015-02-01

    Full Text Available The objective of this paper is to identify investment decision makingschemes using the adequate portfolio model. This approach can be employed to project investment in stocks, using the opportunities offered by the markets and investor intelligence. It was decided to use adequate portfolio theory for investment decision making, simulation of financial markets, and optimisation of utility function. The main conclusion of article suggests investigating return on individual portfolio level. Real investment is a way to make sure of the soundness of applicable strategies.

  5. tRNA evolution from the proto-tRNA minihelix world

    Science.gov (United States)

    Root-Bernstein, Robert; Kim, Yunsoo; Sanjay, Adithya; Burton, Zachary F.

    2016-01-01

    ABSTRACT Multiple models have been advanced for the evolution of cloverleaf tRNA. Here, the conserved archaeal tRNA core (75-nt) is posited to have evolved from ligation of three proto-tRNA minihelices (31-nt) and two-symmetrical 9-nt deletions within joined acceptor stems (93 – 18 = 75-nt). The primary evidence for this conclusion is that the 5-nt stem 7-nt anticodon loop and the 5-nt stem 7-nt T loop are structurally homologous and related by coding sequence. We posit that the D loop was generated from a third minihelix (31-nt) in which the stem and loop became rearranged after 9-nt acceptor stem deletions and cloverleaf folding. The most 3´-5-nt segment of the D loop and the 5-nt V loop are apparent remnants of the joined acceptor stems (14 – 9 = 5-nt). Before refolding in the tRNA cloverleaf, we posit that the 3′-5-nt segment of the D loop and the 5-nt V loop were paired, and, in the tRNA cloverleaf, frequent pairing of positions 29 (D loop) and 47 (V loop) remains (numbered on a 75-nt tRNA cloverleaf core). Amazingly, after >3.5 billion years of evolutionary pressure on the tRNA cloverleaf structure, a model can be constructed that convincingly describes the genesis of 75/75-nt conserved archaeal tRNA core positions. Judging from the tRNA structure, cloverleaf tRNA appears to represent at least a second-generation scheme (and possibly a third-generation scheme) that replaced a robust 31-nt minihelix protein-coding system, evidence for which is preserved in the cloverleaf structure. Understanding tRNA evolution provides insights into ribosome and rRNA evolution. PMID:27636862

  6. tRNA gene diversity in the three domains of life

    Directory of Open Access Journals (Sweden)

    Kosuke eFujishima

    2014-05-01

    Full Text Available Transfer RNA (tRNA is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs possess long variable arms that are specific to eukaryotic class II tRNASer and tRNALeu but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.

  7. Origin, evolution, and mechanism of 5′ tRNA editing in chytridiomycete fungi

    Science.gov (United States)

    LAFOREST, MARIE-JOSÉE; BULLERWELL, CHARLES E.; FORGET, LISE; LANG, B. FRANZ

    2004-01-01

    5′ tRNA editing has been demonstrated to occur in the mitochondria of the distantly related rhizopod amoeba Acanthamoeba castellanii and the chytridiomycete fungus Spizellomyces punctatus. In these organisms, canonical tRNA structures are restored by removing mismatched nucleotides at the first three 5′ positions and replacing them with nucleotides capable of forming Watson–Crick base pairs with their 3′ counterparts. This form of editing seems likely to occur in members of Amoebozoa other than A. castellanii, as well as in members of Heterolobosea. Evidence for 5′ tRNA editing has not been found to date, however, in any other fungus including the deeply branching chytridiomycete Allomyces macrogynus. We predicted that a similar form of tRNA editing would occur in members of the chytridiomycete order Monoblepharidales based on the analysis of complete mitochondrial tRNA complements. This prediction was confirmed by analysis of tRNA sequences using a tRNA circularization/ RT-PCR-based approach. The presence of partially and completely unedited tRNAs in members of the Monoblepharidales suggests the involvement of a 5′-to-3′ exonuclease rather than an endonuclease in removing the three 5′ nucleotides from a tRNA substrate. Surprisingly, analysis of the mtDNA of the chytridiomycete Rhizophydium brooksianum, which branches as a sister group to S. punctatus in molecular phylogenies, did not suggest the presence of editing. This prediction was also confirmed experimentally. The absence of tRNA editing in R. brooksianum raises the possibility that 5′ tRNA editing may have evolved twice independently within Chytridiomycota, once in the lineage leading to S. punctatus and once in the lineage leading to the Monoblepharidales. PMID:15247432

  8. Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major

    Directory of Open Access Journals (Sweden)

    Gowri V S

    2012-11-01

    Full Text Available Abstract Background Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA synthetases, their paralogs and other associated proteins from L. major. Results A total of 26 aminoacyl tRNA synthetases were identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of the L. major aminoacyl tRNA synthetases suggest a probable archaeal/eukaryotic origin. Presence of additional domains or N- or C-terminal extensions in 11 aminoacyl tRNA synthetases from L. major suggests possibilities such as additional tRNA binding or oligomerization or editing activity. Five freestanding editing domains were identified in L. major. Domain assignment revealed a novel asparagine tRNA synthetase paralog, asparagine synthetase A which has been so far reported from prokaryotes and archaea. Conclusions A comprehensive bioinformatic analysis revealed 26 aminoacyl tRNA synthetases and five freestanding editing domains in L. major. Identification of two EMAP (endothelial monocyte-activating polypeptide II-like proteins similar to human EMAP II-like proteins suggests their participation in multisynthetase complex formation. While the phylogeny of tRNA synthetases suggests a probable archaeal/eukaryotic origin, phylogeny of asparagine synthetase A strongly suggests a bacterial origin. The unique features identified in this work provide rationale for designing inhibitors against parasite aminoacyl tRNA synthetases and their paralogs.

  9. Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.

    Science.gov (United States)

    Mihara, Hisaaki; Fujii, Tomomi; Kato, Shin-Ichiro; Kurihara, Tatsuo; Hata, Yasuo; Esaki, Nobuyoshi

    2002-05-01

    Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur.

  10. Defining an Adequate Education for English Learners

    OpenAIRE

    Patricia Gándara; Russell W. Rumberger

    2008-01-01

    This article explores the components of an “adequate” education for linguistic minority students in California and attempts to distinguish these from the components of an adequate education for low-income students who are native English speakers. About 1.6 million students were classified as English learners (ELs) in California in 2006. We argue that in order to determine the costs of educating these students, it is necessary to specify the goals of instruction. Four possible goals are: (1) r...

  11. Interaction of tRNA with domain II of 23S rRNA.

    Science.gov (United States)

    Hill, W E; Tassanakajohn, A; Tapprich, W E

    1990-08-27

    The interaction of tRNA with domain II of 23S rRNA in E. coli ribosomes has been probed using short, complementary DNA oligodeoxyribonucleotides. Specifically, cDNA oligomers to the region 801-811 of the 23S rRNA were used to ascertain the interaction of this region with tRNA. It was found that when tRNA was bound to the P site, considerable competition occurred between tRNA and the cDNA oligomers which base paired with the nucleotides 807-811. However, A-site bound tRNA neither displaced, nor was displaced, by cDNA oligomers to this region. Additionally, the binding of tRNA lacking the CACCA nucleotides on the 3' terminus was unaffected by the presence a cDNA oligomer complementary to nucleotides 803-811, indicating that the cDNA-tRNA competition was dependent on the 3' terminal nucleotides of tRNA.

  12. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Directory of Open Access Journals (Sweden)

    Premal Shah

    2010-09-01

    Full Text Available Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  13. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Science.gov (United States)

    Shah, Premal; Gilchrist, Michael A

    2010-09-16

    Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  14. Ion concentration dependent tRNA folding energy landscapes

    Science.gov (United States)

    Li, Rongzhong; Cho, Samuel

    2013-03-01

    The RNA folding is highly dependent on the ionic conditions of its environment in the cell because the surrounding ions electrostatically screen the charged phosphates that line the RNA backbone. Recent studies (Cho, Pincus, and Thirumalai, PNAS, 2007; Biyun, Cho, and Thirumalai, JACS, 2011) demonstrated that the coarse-grained model we use accurately captures the RNA folding mechanisms by incorporating a Debye-Huckel potential to screen the electrostatics. We compare the ion-concentration dependent tRNA folding mechanism to the classical thermodynamic melting profiles of Crothers and co-workers, and we observe excellent agreement. We also supported our findings by performing empirical force field MD simulations with CHARMM and AMBER, and we observe remarkably comparable qualitative similarities between the average base-base distances from simulations and the empirically measured base-stacking potentials from the well-known Turner's Rules.

  15. Interaction of tRNA with Eukaryotic Ribosome

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer

    2015-03-01

    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.

  16. tRNA and Its Activation Targets as Biomarkers and Regulators of Breast Cancer

    Science.gov (United States)

    2013-09-01

    polymerase III transcripts, including tRNA and 5S rRNA which are directly involved in translation, are found in a wide variety of transformed cell types...scent hypomethylated tRNA and an aberrant form of 5S rRNA . RNA 12: 508–521. Kohrer C, Xie L, Kellerer S, Varshney U, RajBhandary UL. 2001. Import of...We obtained approximately 13 million reads, with 150,000 unique sequences. As expected, a large number of reads map to rRNA and tRNA sequences

  17. The Dynamics of Unfolded versus Folder tRNA: The Role of Electrostatic Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Roh, J H [University of Maryland; Tyagi, M. [NCNR and University of Maryland; Briber, R M [University of Maryland; Woodson, S.A. [Johns Hopkins University; Sokolov, Alexei P [ORNL

    2011-01-01

    The dynamics of RNA contributes to its biological functions such as ligand recognition and catalysis. Using quasielastic neutron scattering spectroscopy, we show that Mg2+ greatly increases the picosecond to nanosecond dynamics of hydrated tRNA while stabilizing its folded structure. Analyses of the atomic mean-squared displacement, relaxation time, persistence length, and fraction of mobile atoms showed that unfolded tRNA is more rigid than folded tRNA. This same result was found for a sulfonated polystyrene, indicating that the increased dynamics in Mg2+ arises from improved charge screening of the polyelectrolyte rather than specific interactions with the folded tRNA. These results are opposite to the relationship between structural compactness and internal dynamics for proteins in which the folded state is more rigid than the denatured state. We conclude that RNA dynamics are strongly influenced by the electrostatic environment, in addition to the motions of local waters.

  18. Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

    Energy Technology Data Exchange (ETDEWEB)

    Dunkle, Jack A.; Wang, Leyi; Feldman, Michael B.; Pulk, Arto; Chen, Vincent B.; Kapral, Gary J.; Noeske, Jonas; Richardson, Jane S.; Blanchard, Scott C.; Cate, Jamie H. Doudna (Cornell); (UCB); (Duke)

    2011-09-06

    During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of {approx}3.2 angstroms by means of 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 and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.

  19. Extensive and evolutionarily persistent mitochondrial tRNA editing in Velvet Worms (phylum Onychophora).

    Science.gov (United States)

    Segovia, Romulo; Pett, Walker; Trewick, Steve; Lavrov, Dennis V

    2011-10-01

    Mitochondrial genomes of onychophorans (velvet worms) present an interesting problem: Some previous studies reported them lacking several transfer RNA (tRNA) genes, whereas others found that all their tRNA genes were present but severely reduced. To resolve this discrepancy, we determined complete mitochondrial DNA (mtDNA) sequences of the onychophorans Oroperipatus sp. and Peripatoides sympatrica as well as cDNA sequences from 14 and 10 of their tRNAs, respectively. We show that tRNA genes in these genomes are indeed highly reduced and encode truncated molecules, which are restored to more conventional structures by extensive tRNA editing. During this editing process, up to 34 nucleotides are added to the tRNA sequences encoded in Oroperipatus sp. mtDNA, rebuilding the aminoacyl acceptor stem, the TΨC arm, and in some extreme cases, the variable arm and even a part of the anticodon stem. The editing is less extreme in P. sympatrica in which at least a part of the TΨC arm is always encoded in mtDNA. When the entire TΨC arm is added de novo in Oroperipatus sp., the sequence of this arm is either identical or similar among different tRNA species, yet the sequences show substantial variation for each tRNA. These observations suggest that the arm is rebuilt, at least in part, by a template-independent mechanism and argue against the alternative possibility that tRNA genes or their parts are imported from the nucleus. By contrast, the 3' end of the aminoacyl acceptor stem is likely restored by a template-dependent mechanism. The extreme tRNA editing reported here has been preserved for >140 My as it was found in both extant families of onychophorans. Furthermore, a similar type of tRNA editing may be present in several other groups of arthropods, which show a high degree of tRNA gene reduction in their mtDNA.

  20. Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives.

    Science.gov (United States)

    Graifer, D M; Babkina, G T; Matasova, N B; Vladimirov, S N; Karpova, G G; Vlassov, V V

    1989-07-01

    A systematic study of protein environment of tRNA in ribosomes in model complexes representing different translation steps was carried out using the affinity labelling of the ribosomes with tRNA derivatives bearing aryl azide groups scattered statistically over tRNA guanine residues. Analysis of the proteins crosslinked to tRNA derivatives showed that the location of the derivatives in the aminoacyl (A) site led to the labelling of the proteins S5 and S7 in all complexes studied, whereas the labelling of the proteins S2, S8, S9, S11, S14, S16, S17, S18, S19, S21 as well as L9, L11, L14, L15, L21, L23, L24, L29 depended on the state of tRNA in A site. Similarly, the location of tRNA derivatives in the peptidyl (P) site resulted in the labelling of the proteins L27, S11, S13 and S19 in all states, whereas the labelling of the proteins S5, S7, S9, S12, S14, S20, S21 as well as L2, L13, L14, L17, L24, L27, L31, L32, L33 depended on the type of complex. The derivatives of tRNA(fMet) were found to crosslink to S1, S3, S5, S7, S9, S14 and L1, L2, L7/L12, L27. Based on the data obtained, a general principle of the dynamic functioning of ribosomes has been proposed: (i) the formation of each type of ribosomal complex is accompanied by changes in mutual arrangement of proteins - 'conformational adjustment' of the ribosome - and (ii) a ribosome can dynamically change its internal structure at each step of initiation and elongation; on the 70 S ribosome there are no rigidly fixed structures forming tRNA-binding sites (primarily A and P sites).

  1. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

    Directory of Open Access Journals (Sweden)

    Miguel M Fonseca

    Full Text Available BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis". PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich. These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".

  2. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection

    Science.gov (United States)

    Zeng, Xiancheng; Chugh, Jeetender; Casiano-Negroni, Anette; Al-Hashimi, Hashim M.; Brooks, Charles L.

    2014-01-01

    Ribosomes control the missense error rate of ~10−4 during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics (MD) simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3 kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4 kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA. PMID:24813122

  3. Effect of PEG and mPEG-anthracene on tRNA aggregation and particle formation.

    Science.gov (United States)

    Froehlich, E; Mandeville, J S; Arnold, D; Kreplak, L; Tajmir-Riahi, H A

    2012-01-09

    Poly(ethylene glycol) (PEG) and its derivatives are synthetic polymers with major applications in gene and drug delivery systems. Synthetic polymers are also used to transport miRNA and siRNA in vitro. We studied the interaction of tRNA with several PEGs of different compositions, such as PEG 3350, PEG 6000, and mPEG-anthracene under physiological conditions. FTIR, UV-visible, CD, and fluorescence spectroscopic methods as well as atomic force microscopy (AFM) were used to analyze the PEG binding mode, the binding constant, and the effects of polymer complexation on tRNA stability, aggregation, and particle formation. Structural analysis showed that PEG-tRNA interaction occurs via RNA bases and the backbone phosphate group with both hydrophilic and hydrophobic contacts. The overall binding constants of K(PEG 3350-tRNA)= 1.9 (±0.5) × 10(4) M(-1), K(PEG 6000-tRNA) = 8.9 (±1) × 10(4) M(-1), and K(mPEG-anthracene)= 1.2 (±0.40) × 10(3) M(-1) show stronger polymer-RNA complexation by PEG 6000 and by PEG 3350 than the mPEG-anthracene. AFM imaging showed that PEG complexes contain on average one tRNA with PEG 3350, five tRNA with PEG 6000, and ten tRNA molecules with mPEG-anthracene. tRNA aggregation and particle formation occurred at high polymer concentrations, whereas it remains in A-family structure.

  4. Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch.

    Science.gov (United States)

    Grigg, Jason C; Ke, Ailong

    2013-12-01

    The term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mRNA. They are typically comprised of separate ligand binding and regulatory domains. The T box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, tRNA. It senses the aminoacylation state of tRNA to regulate genes involved in a variety of functions relating to amino acid metabolism and tRNA aminoacylation. T box riboswitches performs an intuitively simple process using a complex structured RNA element and, until recently, the underlying mechanisms were poorly understood. Only two sequence-specific contacts had been previously identified: (1) between the specifier sequence (codon) and the tRNA anticodon and (2) between an anti-terminator stem loop and the tRNA acceptor arm CCA tail. tRNA aminoacylation blocks the latter interaction and therefore serves as the switch between termination and anti-termination. Outside of these two contacts, the structure and functions of T box riboswitches have come to light in some recent studies. We recently described the X-ray crystal structure of the highly conserved T box riboswitch distal Stem I region and demonstrated that this region interacts with the tRNA elbow to anchor it to the riboswitch. Independently, Lehmann et al. used sequence homology search to arrive at a similar model for Stem I-tRNA interactions. The model was further supported by two recent structures of the Stem I-tRNA complex, determined independently by our group and by Zhang and Ferré-D'Amaré. This article highlights some of these contributions to synthesize an updated model for tRNA recognition by the T box riboswitch.

  5. Enzymatic tRNA acylation by acid and alpha-hydroxy acid analogues of amino acids.

    Science.gov (United States)

    Owczarek, Alina; Safro, Mark; Wolfson, Alexey D

    2008-01-08

    Incorporation of unnatural amino acids with unique chemical functionalities has proven to be a valuable tool for expansion of the functional repertoire and properties of proteins as well as for structure-function analysis. Incorporation of alpha-hydroxy acids (primary amino group is substituted with hydroxyl) leads to the synthesis of proteins with peptide bonds being substituted by ester bonds. Practical application of this modification is limited by the necessity to prepare corresponding acylated tRNA by chemical synthesis. We investigated the possibility of enzymatic incorporation of alpha-hydroxy acid and acid analogues (lacking amino group) of amino acids into tRNA using aminoacyl-tRNA synthetases (aaRSs). We studied direct acylation of tRNAs by alpha-hydroxy acid and acid analogues of amino acids and corresponding chemically synthesized analogues of aminoacyl-adenylates. Using adenylate analogues we were able to enzymatically acylate tRNA with amino acid analogues which were otherwise completely inactive in direct aminoacylation reaction, thus bypassing the natural mechanisms ensuring the selectivity of tRNA aminoacylation. Our results are the first demonstration that the use of synthetic aminoacyl-adenylates as substrates in tRNA aminoacylation reaction may provide a way for incorporation of unnatural amino acids into tRNA, and consequently into proteins.

  6. Is a vegetarian diet adequate for children.

    Science.gov (United States)

    Hackett, A; Nathan, I; Burgess, L

    1998-01-01

    The number of people who avoid eating meat is growing, especially among young people. Benefits to health from a vegetarian diet have been reported in adults but it is not clear to what extent these benefits are due to diet or to other aspects of lifestyles. In children concern has been expressed concerning the adequacy of vegetarian diets especially with regard to growth. The risks/benefits seem to be related to the degree of restriction of he diet; anaemia is probably both the main and the most serious risk but this also applies to omnivores. Vegan diets are more likely to be associated with malnutrition, especially if the diets are the result of authoritarian dogma. Overall, lacto-ovo-vegetarian children consume diets closer to recommendations than omnivores and their pre-pubertal growth is at least as good. The simplest strategy when becoming vegetarian may involve reliance on vegetarian convenience foods which are not necessarily superior in nutritional composition. The vegetarian sector of the food industry could do more to produce foods closer to recommendations. Vegetarian diets can be, but are not necessarily, adequate for children, providing vigilance is maintained, particularly to ensure variety. Identical comments apply to omnivorous diets. Three threats to the diet of children are too much reliance on convenience foods, lack of variety and lack of exercise.

  7. A newly discovered tRNA(1Asp) gene (aspV) of Escherichia coli K12.

    Science.gov (United States)

    Horiuchi, T; Nagasawa, T; Takano, K; Sekiguchi, M

    1987-02-01

    We report a new tRNA(1Asp) gene near the dnaQ gene, which is located at 5 min on the Escherichia coli linkage map. We named it aspV. The sequence corresponding to the mature tRNA is identical with that of the two previously identified tRNA(1Asp) genes (aspT and aspU), but there is no homology in the sequences of their 3'- and 5'-flanking regions.

  8. DNA polymerase ɛ, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator

    OpenAIRE

    Dhillon, Namrita; Raab, Jesse; Guzzo, Julie; Szyjka, Shawn J.; Gangadharan, Sunil; Aparicio, Oscar M.; Andrews, Brenda; Kamakaka, Rohinton T.

    2009-01-01

    Insulators bind transcription factors and use chromatin remodellers and modifiers to mediate insulation. In this report, we identified proteins required for the efficient formation and maintenance of a specialized chromatin structure at the yeast tRNA insulator. The histone acetylases, SAS-I and NuA4, functioned in insulation, independently of tRNA and did not participate in the formation of the hypersensitive site at the tRNA. In contrast, DNA polymerase ɛ, functioned with the chromatin remo...

  9. Informational redundancy of tRNA(4Ser) and tRNA(7Ser) genes in Drosophila melanogaster and evidence for intergenic recombination.

    Science.gov (United States)

    Leung, J; Sinclair, D A; Hayashi, S; Tener, G M; Grigliatti, T A

    1991-05-20

    Variant tRNA genes have been widely observed in multicellular eukaryotes. Recent biochemical studies have shown that some of them are expressed in a tissue- or a stage-specific manner. These findings would thus imply that certain modified tRNAs may be crucial for the development of the organism. Using Drosophila melanogaster as a model, we have taken a combined genetic and molecular approach to examine critically the possible biological functions of tRNA(4, 7Ser) genes. We showed that at least 50% of the total templates can be deleted from the genome without inducing abnormal phenotypes such as Minute, or a decrease in viability. In addition, two of the tRNASer variant genes that are unique in sequence are also completely dispensable. This strongly implies that even though they may be expressed in vivo, they play no essential role in the development of the fruitfly. By comparison with some of the corresponding tRNA genes in another sibling species, Drosophila erecta, our results suggest strongly that the variants are products non-reciprocal exchanges among the tRNA(4, 7Ser), genes. Such intergenic recombination events may have a major influence in the concerted evolution of the two gene families.

  10. Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development.

    Directory of Open Access Journals (Sweden)

    Akiko eSoma

    2014-04-01

    Full Text Available A number of genome analyses and searches using programs that focus on the RNA-specific bulge-helix-bulge (BHB motif have uncovered a wide variety of disrupted tRNA genes. The results of these analyses have shown that genetic information encoding functional RNAs is described in the genome cryptically and is retrieved using various strategies. One such strategy is represented by circularly permuted tRNA genes, in which the sequences encoding the 5′-half and 3′-half of the specific tRNA are separated and inverted on the genome. Biochemical analyses have defined a processing pathway in which the termini of tRNA precursors (pre-tRNAs are ligated to form a characteristic circular RNA intermediate, which is then cleaved at the acceptor-stem to generate the typical cloverleaf structure with functional termini. The sequences adjacent to the processing site located between the 3′-half and the 5′-half of pre-tRNAs potentially form a BHB motif, which is the dominant recognition site for the tRNA-intron splicing endonuclease, suggesting that circularization of pre-tRNAs depends on the splicing machinery. Some permuted tRNAs contain a BHB-mediated intron in their 5′- or 3′-half, meaning that removal of an intron, as well as swapping of the 5′- and 3′-halves, are required during maturation of their pre-tRNAs. To date, 34 permuted tRNA genes have been identified from six species of unicellular algae and one archaeon. Although their physiological significance and mechanism of development remain unclear, the splicing system of BHB motifs seems to have played a key role in the formation of permuted tRNA genes. In this review, current knowledge of circularly permuted tRNA genes is presented and some unanswered questions regarding these species are discussed.

  11. Quality Control Pathways for Nucleus-Encoded Eukaryotic tRNA Biosynthesis and Subcellular Trafficking.

    Science.gov (United States)

    Hopper, Anita K; Huang, Hsiao-Yun

    2015-06-01

    tRNAs perform an essential role in translating the genetic code. They are long-lived RNAs that are generated via numerous posttranscriptional steps. Eukaryotic cells have evolved numerous layers of quality control mechanisms to ensure that the tRNAs are appropriately structured, processed, and modified. We describe the known tRNA quality control processes that check tRNAs and correct or destroy aberrant tRNAs. These mechanisms employ two types of exonucleases, CCA end addition, tRNA nuclear aminoacylation, and tRNA subcellular traffic. We arrange these processes in order of the steps that occur from generation of precursor tRNAs by RNA polymerase (Pol) III transcription to end maturation and modification in the nucleus to splicing and additional modifications in the cytoplasm. Finally, we discuss the tRNA retrograde pathway, which allows tRNA reimport into the nucleus for degradation or repair. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Calcium regulates the expression of a Dictyostelium discoideum asparaginyl tRNA synthetase gene

    Indian Academy of Sciences (India)

    Jyoti K Jaiswal; Vidyanand Nanjundiah

    2003-12-01

    In a screen for calcium-regulated gene expression during growth and development of Dictyostelium discoideum we have identified an asparaginyl tRNA synthetase (ddAsnRS) gene, the second tRNA synthetase gene identified in this organism. The ddAsnRS gene shows many unique features. One, it is repressed by lowering cellular calcium, making it the first known calcium-regulated tRNA synthetase. Two, despite the calcium-dependence, its expression is unaltered during the cell cycle, making this the first D. discoideum gene to show a calcium-dependent but cell cycle phase-independent expression. Finally, the N-terminal domain of the predicted ddAsnRS protein shows higher sequence similarity to Glutaminyl tRNA synthetases than to other Asn tRNA synthetases. These unique features of the AsnRS from this primitive eukaryote not only point to a novel mechanism regulating the components of translation machinery and gene expression by calcium, but also hint at a link between the evolution of GlnRS and AsnRS in eukaryotes.

  13. tRNA modification profiles of the fast-proliferating cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Chao; Niu, Leilei; Song, Wei [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China); Xiong, Xin; Zhang, Xianhua [Departmentof Pharmacy, Peking University Third Hospital, Peking University, Beijing 100191 (China); Zhang, Zhenxi; Yang, Yi; Yi, Fan [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China); Zhan, Jun; Zhang, Hongquan [Department of Anatomy, Histology and Embryology, Laboratory of Molecular Cell Biology and Tumor Biology, Peking University, Beijing 100191 (China); Yang, Zhenjun; Zhang, Li-He [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China); Zhai, Suodi [Departmentof Pharmacy, Peking University Third Hospital, Peking University, Beijing 100191 (China); Li, Hua, E-mail: huali88@sina.com [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China); Ye, Min, E-mail: yemin@bjmu.edu.cn [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China); Du, Quan, E-mail: quan.du@pku.edu.cn [State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Department of Obstetrics and Gynecology, Peking University Third Hospital, Peking University, Beijing 100191 (China)

    2016-08-05

    Despite the recent progress in RNA modification study, a comprehensive modification profile is still lacking for mammalian cells. Using a quantitative HPLC/MS/MS assay, we present here a study where RNA modifications are examined in term of the major RNA species. With paired slow- and fast-proliferating cell lines, distinct RNA modification profiles are first revealed for diverse RNA species. Compared to mRNAs, increased ribose and nucleobase modifications are shown for the highly-structured tRNAs and rRNAs, lending support to their contribution to the formation of high-order structures. This study also reveals a dynamic tRNA modification profile in the fast-proliferating cells. In addition to cultured cells, this unique tRNA profile has been further confirmed with endometrial cancers and their adjacent normal tissues. Taken together, the results indicate that tRNA is a actively regulated RNA species in the fast-proliferating cancer cells, and suggest that they may play a more active role in biological process than expected. -- Highlights: •RNA modifications were first examined in term of the major RNA species. •A dynamic tRNA modifications was characterized for the fast-proliferating cells. •The unique tRNA profile was confirmed with endometrial cancers and their adjacent normal tissues. •tRNA was predicted as an actively regulated RNA species in the fast-proliferating cancer cells.

  14. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease.

    Science.gov (United States)

    Kirchner, Sebastian; Ignatova, Zoya

    2015-02-01

    tRNAs, nexus molecules between mRNAs and proteins, have a central role in translation. Recent discoveries have revealed unprecedented complexity of tRNA biosynthesis, modification patterns, regulation and function. In this Review, we present emerging concepts regarding how tRNA abundance is dynamically regulated and how tRNAs (and their nucleolytic fragments) are centrally involved in stress signalling and adaptive translation, operating across a wide range of timescales. Mutations in tRNAs or in genes affecting tRNA biogenesis are also linked to complex human diseases with surprising heterogeneity in tissue vulnerability, and we highlight cell-specific aspects that modulate the disease penetrance of tRNA-based pathologies.

  15. Saturation of recognition elements blocks evolution of new tRNA identities.

    Science.gov (United States)

    Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A; Ribas de Pouplana, Lluís

    2016-04-01

    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure.

  16. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases

    Directory of Open Access Journals (Sweden)

    Kozo eTomita

    2014-02-01

    Full Text Available The universal 3'-terminal CCA sequence of tRNA is built and/or synthesized by the CCA-adding enzyme, CTP:(ATP tRNA nucleotidyltransferase. This RNA polymerase has no nucleic acid template, but faithfully synthesizes the defined CCA sequence on the 3'-terminus of tRNA at one time, using CTP and ATP as substrates. The mystery of CCA-addition without a nucleic acid template by unique RNA polymerases has long fascinated researchers in the field of RNA enzymology. In this review, the mechanisms of RNA polymerization by the remarkable CCA-adding enzyme and its related enzymes are presented, based on their structural features.

  17. Dynamical analysis of tRNA Gln-GlnRS complex using normal mode calculation

    Science.gov (United States)

    Nakamura, Shugo; Ikeguchi, Mitsunori; Shimizu, Kentaro

    2003-04-01

    We applied normal mode calculation in internal coordinates to a complex of glutamine transfer RNA (tRNA Gln) and glutaminyl-tRNA synthetase (GlnRS). Calculated deviations of atoms agreed well with those obtained from X-ray data. The differences of motions corresponding to low mode frequencies between the free state and the complex state were analyzed. For GlnRS, many motions in the free state were conserved in the complex state, while the dynamics of tRNA Gln was largely affected by the complex formation. Superimposed images of the conserved and non-conserved motions of tRNA Gln clearly indicated the restricted direction of motions in the complex.

  18. A voltage-gated pore for translocation of tRNA

    Energy Technology Data Exchange (ETDEWEB)

    Koley, Sandip; Adhya, Samit, E-mail: nilugrandson@gmail.com

    2013-09-13

    Highlights: •A tRNA translocating complex was assembled from purified proteins. •The complex translocates tRNA at a membrane potential of ∼60 mV. •Translocation requires Cys and His residues in the Fe–S center of RIC6 subunit. -- Abstract: Very little is known about how nucleic acids are translocated across membranes. The multi-subunit RNA Import Complex (RIC) from mitochondria of the kinetoplastid protozoon Leishmania tropica induces translocation of tRNAs across artificial or natural membranes, but the nature of the translocation pore remains unknown. We show that subunits RIC6 and RIC9 assemble on the membrane in presence of subunit RIC4A to form complex R3. Atomic Force Microscopy of R3 revealed particles with an asymmetric surface groove of ∼20 nm rim diameter and ∼1 nm depth. R3 induced translocation of tRNA into liposomes when the pH of the medium was lowered to ∼6 in the absence of ATP. R3-mediated tRNA translocation could also be induced at neutral pH by a K{sup +} diffusion potential with an optimum of 60–70 mV. Point mutations in the Cys{sub 2}–His{sub 2} Fe-binding motif of RIC6, which is homologous to the respiratory Complex III Fe–S protein, abrogated import induced by low pH but not by K{sup +} diffusion potential. These results indicate that the R3 complex forms a pore that is gated by a proton-generated membrane potential and that the Fe–S binding region of RIC6 has a role in proton translocation. The tRNA import complex of L. tropica thus contains a novel macromolecular channel distinct from the mitochondrial protein import pore that is apparently involved in tRNA import in some species.

  19. Abundant Semigroups Which Are Disjoint Unions of Multiplicative Adequate Transversals

    Institute of Scientific and Technical Information of China (English)

    Haijun LIU; Xiaojiang GUO

    2013-01-01

    The aim of this paper is to study abundant semigroups which are disjoint unions of multiplicative adequate tranversals.After obtaining some properties of such semigroup,we prove that a semigroup is a disjoint union of multiplicative adequate transversals if and only if it is isomorphic to the direct product of a rectangular band and an adequate semigroup.

  20. Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10

    Science.gov (United States)

    Swinehart, William E.; Henderson, Jeremy C.; Jackman, Jane E.

    2013-01-01

    N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m1G9 modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m1G9 containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wild-type yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing. PMID:23793893

  1. Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding.

    Science.gov (United States)

    Pinker, Franziska; Schelcher, Cédric; Fernandez-Millan, Pablo; Gobert, Anthony; Birck, Catherine; Thureau, Aurélien; Roblin, Pierre; Giegé, Philippe; Sauter, Claude

    2017-08-25

    RNase P is a universal enzyme that removes 5' leader sequences from tRNA precursors. The enzyme is therefore essential for maturation of functional tRNAs and mRNA translation. RNase P represents a unique example of an enzyme that can occur either as ribonucleoprotein or as protein alone. The latter form of the enzyme, called protein-only RNase P (PRORP), is widespread in eukaryotes in which it can provide organellar or nuclear RNase P activities. Here, we have focused on Arabidopsis nuclear PRORP2 and its interaction with tRNA substrates. Affinity measurements helped assess the respective importance of individual pentatricopeptide repeat motifs in PRORP2 for RNA binding. We characterized the PRORP2 structure by X-ray crystallography and by small-angle X-ray scattering in solution as well as that of its complex with a tRNA precursor by small-angle X-ray scattering. Of note, our study reports the first structural data of a PRORP-tRNA complex. Combined with complementary biochemical and biophysical analyses, our structural data suggest that PRORP2 undergoes conformational changes to accommodate its substrate. In particular, the catalytic domain and the RNA-binding domain can move around a central hinge. Altogether, this work provides a refined model of the PRORP-tRNA complex that illustrates how protein-only RNase P enzymes specifically bind tRNA and highlights the contribution of protein dynamics to achieve this specific interaction. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. A Class of Left E-adequate Semigroups

    Institute of Scientific and Technical Information of China (English)

    LI YONG-HUA; HE YONG

    2010-01-01

    In this paper we establish a construction of a class of left E-adequate semigroups by using semilattices of cancellative monoids and fundamental left E-adequate semigroups. We first introduce concepts of type μ+ (μ*, μ) abundant semigroups and type μ+ left E-adequate semigroups. In fact, regular semigroups are type μ+ abundant semigroups and inverse semigroups are type μ+ left E-adequate semigroups. Next, we construct a special kind of algebras called E+-product. It is proved that every E+-product is a type μ+ left E-adequate semigroup, and every type μ+ left E-adequate semigroup is isomorphic to an E+-product of a semilattice of cancellative monoids with a fundamental left E-adequate semigroup. Finally, as a corollary of the main result, it is deduced that every inverse semigroup is isomorphic to an E+-product of a Clifford semigroup by a fundamental inverse semigroup.

  3. Insights on the mechanism of thioredoxin reductase inhibition by gold N-heterocyclic carbene compounds using the synthetic linear selenocysteine containing C-terminal peptide hTrxR(488-499): an ESI-MS investigation.

    Science.gov (United States)

    Pratesi, Alessandro; Gabbiani, Chiara; Michelucci, Elena; Ginanneschi, Mauro; Papini, Anna Maria; Rubbiani, Riccardo; Ott, Ingo; Messori, Luigi

    2014-07-01

    Gold-based drugs typically behave as strong inhibitors of the enzyme thioredoxin reductase (hTrxR), possibly as the consequence of direct Gold(I) coordination to its active site selenocysteine. To gain a deeper insight into the molecular basis of enzyme inhibition and prove gold-selenocysteine coordination, the reactions of three parent Gold(I) NHC compounds with the synthetic C-terminal dodecapeptide of hTrxR containing Selenocysteine at position 498, were investigated by electrospray ionization mass spectrometry (ESI-MS). Formation of 1:1 Gold-peptide adducts, though in highly different amounts, was demonstrated in all cases. In these adducts the same [Au-NHC](+) moiety is always associated to the intact peptide. Afterward, tandem MS experiments, conducted on a specific Gold-peptide complex, pointed out that Gold is coordinated to the selenolate group. The relatively large strength of the Gold-selenolate coordinative bond well accounts for potent enzyme inhibition typically afforded by these Gold(I) compounds. In a selected case, the time course of enzyme inhibition was explored. Interestingly, enzyme inhibition turned out to show up very quickly and reached its maximum just few minutes after mixing. Overall, the present results offer some clear insight into the process of thioredoxin reductase inhibition by Gold-based compounds. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry.

    Science.gov (United States)

    Carter, Charles W; Wolfenden, Richard

    2016-01-01

    The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology.

  5. Machine News and Volatility: The Dow Jones Industrial Average and the TRNA Sentiment Series

    NARCIS (Netherlands)

    D.E. Allen (David); A.K. Singh (Abhay)

    2014-01-01

    markdownabstract__Abstract__ This paper features an analysis of the relationship between the volatility of the Dow Jones Industrial Average (DJIA) Index and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA) provided by SIRCA (The Securities Industry Re

  6. HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency

    Science.gov (United States)

    van Weringh, Anna; Ragonnet-Cronin, Manon; Pranckeviciene, Erinija; Pavon-Eternod, Mariana; Kleiman, Lawrence; Xia, Xuhua

    2011-01-01

    Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNALys needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding codons that are highly used by HIV-1 but avoided by its host are overrepresented in HIV-1 virions. In particular, tRNAs decoding A-ending codons, required for the expression of HIV's A-rich genome, are highly enriched. Because the affinity of Gag-Pol for all tRNAs is nonspecific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Codon usage of HIV-1 early genes is similar to that of highly expressed host genes, but codon usage of HIV-1 late genes was better adapted to the selectively enriched tRNA pool, suggesting that alterations in the tRNA pool are induced late in viral infection. If HIV-1 genes are adapting to an altered tRNA pool, codon adaptation of HIV-1 may be better than previously thought. PMID:21216840

  7. An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

    Science.gov (United States)

    Cedergren, R J

    1982-04-01

    Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

  8. A correlation between N2-dimethylguanosine presence and alternate tRNA conformers.

    Science.gov (United States)

    Steinberg, S; Cedergren, R

    1995-11-01

    Even though the evolutionary conservation of the cloverleaf model is strongly suggestive of powerful constraints on the secondary structure of functional tRNAs, some mitochondrial tRNAs cannot be folded into this form. From the optimal base pairing pattern of these recalcitrant tRNAs, structural correlations between the length of the anticodon stem and the lengths of connector regions between the two helical domains, formed by the coaxial stacking of the anticodon and D-stems and the acceptor and T-stems, have been derived and used to scan the tRNA and tRNA gene database. We show here that some cytosolic tRNA gene sequences that are compatible with the cloverleaf model can also be folded into patterns proposed for the unusual mitochondrial tRNAs. Furthermore, the ability to be folded into these atypical structures correlates in the mature RNA sequences with the presence of dimethylguanosine, whose role may be to prevent the unusual mitochondrial tRNA pattern folding.

  9. Protozoan ALKBH8 Oxygenases Display both DNA Repair and tRNA Modification Activities

    DEFF Research Database (Denmark)

    Zdżalik, Daria; Vågbø, Cathrine B; Kirpekar, Finn

    2014-01-01

    , interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function...

  10. Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.

    Science.gov (United States)

    Fujii, T; Maeda, M; Mihara, H; Kurihara, T; Esaki, N; Hata, Y

    2000-02-15

    Escherichia coli CsdB, a NifS homologue with a high specificity for L-selenocysteine, is a pyridoxal 5'-phosphate (PLP)-dependent dimeric enzyme that belongs to aminotransferases class V in fold-type I of PLP enzymes and catalyzes the decomposition of L-selenocysteine into selenium and L-alanine. The crystal structure of the enzyme has been determined by the X-ray crystallographic method of multiple isomorphous replacement and refined to an R-factor of 18.7% at 2.8 A resolution. The subunit structure consists of three parts: a large domain of an alpha/beta-fold containing a seven-stranded beta-sheet flanked by seven helices, a small domain containing a four-stranded antiparallel beta-sheet flanked by three alpha-helices, and an N-terminal segment containing two alpha-helices. The overall fold of the subunit is similar to those of the enzymes belonging to the fold-type I family represented by aspartate aminotransferase. However, CsdB has several structural features that are not observed in other families of the enzymes. A remarkable feature is that an alpha-helix in the lobe extending from the small domain to the large domain in one subunit of the dimer interacts with a beta-hairpin loop protruding from the large domain of the other subunit. The extended lobe and the protruded beta-hairpin loop form one side of a limb of each active site in the enzyme. The most striking structural feature of CsdB lies in the location of a putative catalytic residue; the side chain of Cys364 on the extended lobe of one subunit is close enough to interact with the gamma-atom of a modeled substrate in the active site of the subunit. Moreover, His55 from the other subunit is positioned so that it interacts with the gamma- or beta-atom of the substrate and may be involved in the catalytic reaction. This is the first report on three-dimensional structures of NifS homologues.

  11. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    Science.gov (United States)

    Zhang, Gong; Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya

    2011-04-01

    In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.

  12. Mitochondrial tRNA cleavage by tRNA-targeting ribonuclease causes mitochondrial dysfunction observed in mitochondrial disease

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Tetsuhiro, E-mail: atetsu@mail.ecc.u-tokyo.ac.jp; Shimizu, Ayano; Takahashi, Kazutoshi; Hidaka, Makoto; Masaki, Haruhiko, E-mail: amasaki@mail.ecc.u-tokyo.ac.jp

    2014-08-15

    Highlights: • MTS-tagged ribonuclease was translocated successfully to the mitochondrial matrix. • MTS-tagged ribonuclease cleaved mt tRNA and reduced COX activity. • Easy and reproducible method of inducing mt tRNA dysfunction. - Abstract: Mitochondrial DNA (mtDNA) is a genome possessed by mitochondria. Since reactive oxygen species (ROS) are generated during aerobic respiration in mitochondria, mtDNA is commonly exposed to the risk of DNA damage. Mitochondrial disease is caused by mitochondrial dysfunction, and mutations or deletions on mitochondrial tRNA (mt tRNA) genes are often observed in mtDNA of patients with the disease. Hence, the correlation between mt tRNA activity and mitochondrial dysfunction has been assessed. Then, cybrid cells, which are constructed by the fusion of an enucleated cell harboring altered mtDNA with a ρ{sup 0} cell, have long been used for the analysis due to difficulty in mtDNA manipulation. Here, we propose a new method that involves mt tRNA cleavage by a bacterial tRNA-specific ribonuclease. The ribonuclease tagged with a mitochondrial-targeting sequence (MTS) was successfully translocated to the mitochondrial matrix. Additionally, mt tRNA cleavage, which resulted in the decrease of cytochrome c oxidase (COX) activity, was observed.

  13. Pentamidine binds to tRNA through non-specific hydrophobic interactions and inhibits aminoacylation and translation.

    Science.gov (United States)

    Sun, Tao; Zhang, Yi

    2008-03-01

    The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrated that pentamidine non-specifically binds to two distinct classes of sites on tRNA. The binding was driven by favorable entropy changes indicative of a large hydrophobic interaction, suggesting that the aromatic rings of pentamidine are inserted into the stacked base pairs of tRNA helices. Pentamidine binding disrupts the tRNA secondary structure and masks the anticodon loop in the tertiary structure. Consistently, we showed that pentamidine specifically inhibits tRNA aminoacylation but not the cognate amino acid adenylation. Pentamidine inhibited protein translation in vitro with an EC(50) equivalent to that binds to tRNA and inhibits tRNA aminoacylation in vitro, but drastically higher than that inhibits translation in vivo, supporting the established notion that the antimicrobial activity of pentamidine is largely due to its selective accumulation by the pathogen rather than by the host cell. Therefore, interrupting tRNA aminoacylation by the entropy-driven non-specific binding is an important mechanism of pentamidine in inhibiting protein translation, providing new insights into the development of antimicrobial drugs.

  14. Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t.

    Science.gov (United States)

    Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

    2016-03-29

    Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

  15. Structural rules and conformational compensations in the tRNA L-form.

    Science.gov (United States)

    Steinberg, S; Leclerc, F; Cedergren, R

    1997-02-21

    The mitochondrial tRNAs (mtRNA) of five distinct, secondary structure types have been identified in the tRNA sequence compilation, and the three-dimensional modeling for representative sequences of these types has been carried out using a new criterion for the lengths of the helical domains and connector regions in a full-sized tRNA conformation. This criterion has been derived from the analysis of the known structures of cytosolic tRNAs and states that in the tRNA structure nucleotide 59 of the T-loop should stack onto Domain 1. To ensure this, Domain 1 must have 12 layers of stacked nucleotides, and in the case of a deletion of a base-pair in the T-stem, an additional 13th layer is required. Although a number of mitochondrial tRNAs harbored deficiencies in this criterion and, therefore, could not be modeled directly, this disability could be corrected and modeling accomplished by invoking structural compensations derived from one of two unusual aspects of these tRNAs. One class of these tRNAs contained an unpaired nucleotide in their anticodon stem, and their three-dimensional structure was successfully modeled when the unpaired nucleotide was intercalated into the helical domain of the stem. The second class contained more than the required number of nucleotides connecting the tRNA helical domains; the conformational flexibility of these nucleotides allowed them to take the place of the absent layers. The conformational compensation that we report rationalizes disparate features of these tRNAs and suggests that the stacking of nucleotide 59 on Domain 1 is an essential feature of the three-dimensional L-form of tRNA.

  16. Evolution meets disease: penetrance and functional epistasis of mitochondrial tRNA mutations.

    Science.gov (United States)

    Moreno-Loshuertos, Raquel; Ferrín, Gustavo; Acín-Pérez, Rebeca; Gallardo, M Esther; Viscomi, Carlo; Pérez-Martos, Acisclo; Zeviani, Massimo; Fernández-Silva, Patricio; Enríquez, José Antonio

    2011-04-01

    About half of the mitochondrial DNA (mtDNA) mutations causing diseases in humans occur in tRNA genes. Particularly intriguing are those pathogenic tRNA mutations than can reach homoplasmy and yet show very different penetrance among patients. These mutations are scarce and, in addition to their obvious interest for understanding human pathology, they can be excellent experimental examples to model evolution and fixation of mitochondrial tRNA mutations. To date, the only source of this type of mutations is human patients. We report here the generation and characterization of the first mitochondrial tRNA pathological mutation in mouse cells, an m.3739G>A transition in the mitochondrial mt-Ti gene. This mutation recapitulates the molecular hallmarks of a disease-causing mutation described in humans, an m.4290T>C transition affecting also the human mt-Ti gene. We could determine that the pathogenic molecular mechanism, induced by both the mouse and the human mutations, is a high frequency of abnormal folding of the tRNA(Ile) that cannot be charged with isoleucine. We demonstrate that the cells harboring the mouse or human mutant tRNA have exacerbated mitochondrial biogenesis triggered by an increase in mitochondrial ROS production as a compensatory response. We propose that both the nature of the pathogenic mechanism combined with the existence of a compensatory mechanism can explain the penetrance pattern of this mutation. This particular behavior can allow a scenario for the evolution of mitochondrial tRNAs in which the fixation of two alleles that are individually deleterious can proceed in two steps and not require the simultaneous mutation of both.

  17. Binding of tRNA nucleotidyltransferase to Affi-Gel Blue: rapid purification of the enzyme and binding studies.

    Science.gov (United States)

    Deutscher, M P; Masiakowski, P

    1978-06-01

    Rabbit liver tRNA nucleotidyldransferase bound to columns of Affi-Gel Blue and could be specifically eluted with tRNA. This observation led to development of a rapid purification procedure for the enzyme. The adsorbent was also used to assess interaction of tRNA nucleotidyltransferase with various polynucleotides and substrates. The enzyme could be efficiently desorbed from Affi-Gel Blue by low concentrations of tRNA-C-C, less well by tRNA-C-C-A, and not at all by poly(A), poly(C), ATP or CTP.

  18. Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: identification of new functional tRNA primers in murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Pedersen, F S

    2000-01-01

    . While most of the selected primer binding sites are complementary to the 3'-end of tRNA((Pro)), we also retrieved PBS sequences matching four other tRNA molecules and demonstrate that Akv murine leukemia virus vectors may efficiently replicate using tRNA(Arg(CCU)), tRNA(Phe(GAA))and a hitherto unknown......Retroviral reverse transcription is initiated from a cellular tRNA molecule and all known exogenous isolates of murine leukemia virus utilise a tRNA(Pro)molecule. While several studies suggest flexibility in murine leukemia virus primer utilisation, studies on human immunodeficiency virus and avian...... retro-viruses have revealed evidence of molecular adapt-ation towards the specific tRNA isoacceptor used as replication primer. In this study, murine leukemia virus tRNA utilisation is investigated by in vivo screening of a retroviral vector combinatorial library with randomised primer binding sites...

  19. 10 CFR 503.35 - Inability to obtain adequate capital.

    Science.gov (United States)

    2010-01-01

    ... capital investment, through tariffs, without unreasonably adverse economic effect on its service area... 10 Energy 4 2010-01-01 2010-01-01 false Inability to obtain adequate capital. 503.35 Section 503... New Facilities § 503.35 Inability to obtain adequate capital. (a) Eligibility. Section 212(a)(1)(D)...

  20. 13 CFR 108.200 - Adequate capital for NMVC Companies.

    Science.gov (United States)

    2010-01-01

    ... VENTURE CAPITAL (âNMVCâ) PROGRAM Qualifications for the NMVC Program Capitalizing A Nmvc Company § 108.200 Adequate capital for NMVC Companies. You must meet the requirements of §§ 108.200-108.230 in order to... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Adequate capital for...

  1. 9 CFR 305.3 - Sanitation and adequate facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  2. 40 CFR 716.25 - Adequate file search.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Adequate file search. 716.25 Section 716.25 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT HEALTH AND SAFETY DATA REPORTING General Provisions § 716.25 Adequate file search. The scope of a...

  3. Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies

    Science.gov (United States)

    Islam, Md. Maidul; Pandya, Prateek; Chowdhury, Sebanti Roy; Kumar, Surat; Kumar, Gopinatha Suresh

    2008-11-01

    The interaction of two natural protoberberine plant alkaloids berberine and palmatine with tRNA phe was studied using various biophysical techniques and molecular modeling and the data were compared with the binding of the classical DNA intercalator, ethidium. Circular dichroic studies revealed that the tRNA conformation was moderately perturbed on binding of the alkaloids. The cooperative binding of both the alkaloids and ethidium to tRNA was revealed from absorbance and fluorescence studies. Fluorescence quenching studies advanced a conclusion that while berberine and palmatine are partially intercalated, ethidium is fully intercalated on the tRNA molecule. The binding of the alkaloids as well as ethidium stabilized the tRNA melting, and the binding constant evaluated from the averaged optical melting temperature data was in agreement with fluorescence spectral-binding data. Differential scanning calorimetry revealed that the tRNA melting showed three close transitions that were affected on binding of these small molecules. Molecular docking calculations performed showed the preferred regions of binding of these small molecules on the tRNA. Taken together, the results suggest that the binding of the alkaloids berberine and palmatine on the tRNA structure appears to be mostly by partial intercalation while ethidium intercalates fully on the tRNA. These results further advance our knowledge on the molecular aspects on the interaction of these alkaloids to tRNA.

  4. RNA fragments mimicking tRNA analogs interact with cytochrome c.

    Science.gov (United States)

    Pawlowska, Roza; Janicka, Magdalena; Jedrzejczyk, Dominika; Chworos, Arkadiusz

    2016-04-01

    In times, when drug seeking assays focus on the natural molecular triggers and their analogs, a deeper insight into molecular mechanisms governing the initial step of intrinsic apoptosis (cytochrome c release) is essential to suppress the immortality of pathologically changed cells. In this study, we examined RNA molecules mimicking mitochondrial tRNAs interacting with cytochrome c and possibly affecting its cellular function. tRNA analogs were designed and synthesized prior to the conformational analysis and gel assays clearly stating the nucleic acid-protein complex formation. The circular dichroism spectroscopic (CD) and microscale thermophoresis examination revealed the structural and conformational differences between four tRNA analogs in their interactions with cytochrome c. Obtained CD spectra and gel studies resulted in the complex ratio estimation and conclusion that not only the complex formation may be preferential towards specific tRNAs present in the cell, but nucleobase modifications are not essential for such interaction.

  5. let-65 is cytoplasmic methionyl tRNA synthetase in C. elegans

    Directory of Open Access Journals (Sweden)

    Maha Z. Alriyami

    2014-12-01

    Full Text Available Cytoplasmic methionyl tRNA synthetase (MetRS is one of more than 20 cytoplasmic aminoacyl tRNA synthetase enzymes (ARS. This family of enzymes catalyzes a process fundamental for protein translation. Using a combination of genetic mapping, oligonucleotide array comparative genomic hybridization, and phenotypic correlation, we show that mutations in the essential gene, let-65, reside within the predicted Caenorhabditis elegans homologue of MetRS, which we have named mars-1. We demonstrate that the lethality associated with alleles of let-65 is fully rescued by a transgenic array that spans the mars-1 genomic region. Furthermore, sequence analysis reveals that six let-65 alleles lead to the alteration of highly conserved amino acids.

  6. tRNA modifying enzymes, NSUN2 and METTL1, determine sensitivity to 5-fluorouracil in HeLa cells.

    Directory of Open Access Journals (Sweden)

    Mayumi Okamoto

    2014-09-01

    Full Text Available Nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay (RTD. The tRNA modifying enzymes, NSUN2 and METTL1, are mammalian orthologs of yeast Trm4 and Trm8, which are required for protecting tRNA against RTD. A simultaneous overexpression of NSUN2 and METTL1 is widely observed among human cancers suggesting that targeting of both proteins provides a novel powerful strategy for cancer chemotherapy. Here, we show that combined knockdown of NSUN2 and METTL1 in HeLa cells drastically potentiate sensitivity of cells to 5-fluorouracil (5-FU whereas heat stress of cells revealed no effects. Since NSUN2 and METTL1 are phosphorylated by Aurora-B and Akt, respectively, and their tRNA modifying activities are suppressed by phosphorylation, overexpression of constitutively dephosphorylated forms of both methyltransferases is able to suppress 5-FU sensitivity. Thus, NSUN2 and METTL1 are implicated in 5-FU sensitivity in HeLa cells. Interfering with methylation of tRNAs might provide a promising rationale to improve 5-FU chemotherapy of cancer.

  7. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.

    Science.gov (United States)

    Abe, Takashi; Inokuchi, Hachiro; Yamada, Yuko; Muto, Akira; Iwasaki, Yuki; Ikemura, Toshimichi

    2014-01-01

    The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

  8. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data

    Directory of Open Access Journals (Sweden)

    Takashi eAbe

    2014-05-01

    Full Text Available The tRNA Gene Data Base Curated by Experts tRNADB-CE (http://trna.ie.niigata-u.ac.jp was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses’, 121 chloroplasts’, and 12 eukaryotes’ genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that BLSOM with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

  9. DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator.

    Science.gov (United States)

    Dhillon, Namrita; Raab, Jesse; Guzzo, Julie; Szyjka, Shawn J; Gangadharan, Sunil; Aparicio, Oscar M; Andrews, Brenda; Kamakaka, Rohinton T

    2009-09-02

    Insulators bind transcription factors and use chromatin remodellers and modifiers to mediate insulation. In this report, we identified proteins required for the efficient formation and maintenance of a specialized chromatin structure at the yeast tRNA insulator. The histone acetylases, SAS-I and NuA4, functioned in insulation, independently of tRNA and did not participate in the formation of the hypersensitive site at the tRNA. In contrast, DNA polymerase epsilon, functioned with the chromatin remodeller, Rsc, and the histone acetylase, Rtt109, to generate a histone-depleted region at the tRNA insulator. Rsc and Rtt109 were required for efficient binding of TFIIIB to the tRNA insulator, and the bound transcription factor and Rtt109 in turn were required for the binding of Rsc to tRNA. Robust insulation during growth and cell division involves the formation of a hypersensitive site at the insulator during chromatin maturation together with competition between acetylases and deacetylases.

  10. RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification.

    Directory of Open Access Journals (Sweden)

    Aneeshkumar G Arimbasseri

    2015-12-01

    Full Text Available Control of the differential abundance or activity of tRNAs can be important determinants of gene regulation. RNA polymerase (RNAP III synthesizes all tRNAs in eukaryotes and it derepression is associated with cancer. Maf1 is a conserved general repressor of RNAP III under the control of the target of rapamycin (TOR that acts to integrate transcriptional output and protein synthetic demand toward metabolic economy. Studies in budding yeast have indicated that the global tRNA gene activation that occurs with derepression of RNAP III via maf1-deletion is accompanied by a paradoxical loss of tRNA-mediated nonsense suppressor activity, manifested as an antisuppression phenotype, by an unknown mechanism. We show that maf1-antisuppression also occurs in the fission yeast S. pombe amidst general activation of RNAP III. We used tRNA-HydroSeq to document that little changes occurred in the relative levels of different tRNAs in maf1Δ cells. By contrast, the efficiency of N2,N2-dimethyl G26 (m(22G26 modification on certain tRNAs was decreased in response to maf1-deletion and associated with antisuppression, and was validated by other methods. Over-expression of Trm1, which produces m(22G26, reversed maf1-antisuppression. A model that emerges is that competition by increased tRNA levels in maf1Δ cells leads to m(22G26 hypomodification due to limiting Trm1, reducing the activity of suppressor-tRNASerUCA and accounting for antisuppression. Consistent with this, we show that RNAP III mutations associated with hypomyelinating leukodystrophy decrease tRNA transcription, increase m(22G26 efficiency and reverse antisuppression. Extending this more broadly, we show that a decrease in tRNA synthesis by treatment with rapamycin leads to increased m(22G26 modification and that this response is conserved among highly divergent yeasts and human cells.

  11. The core domain of Aquifex aeolicus tRNA (m7G46) methyltransferase has the methyl-transfer activity to tRNA.

    Science.gov (United States)

    Tomikawa, Chie; Hori, Hiroyuki

    2006-01-01

    Transfer RNA (m(7)G46) methyltransferase [TrmB] catalyses the transfer of methyl groups from S-adenosyl-L-methionine to the N(7)-atom of guanine at position 46 in tRNA. TrmB proteins from thermophilic bacteria such as Aquifex aeolicus have a long C-terminal region as compared to those from mesophilic bacteria. Further, N-terminal region observed in TrmB proteins from mesophiles is missing in A. aeolicus TrmB. Therefore, we considered that this distinct C-terminal region in A. aeolicus TrmB might compensate the N-terminal region in mesophile TrmB and function as a part of tRNA binding site. To confirm this idea, we deleted the C-terminal region by introduction of the stop codon at position 202. To our surprise, methyl-transfer assay using yeast tRNA(Phe) transcript clearly showed that the resultant mutant protein (Glu202Stop) had an enzymatic activity. Thus, the core domain of the A. aeolicus TrmB has a methyl-transfer activity.

  12. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

    Science.gov (United States)

    Fernández-Calero, Tamara; Cabrera-Cabrera, Florencia; Ehrlich, Ricardo; Marín, Mónica

    2016-01-01

    Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process. PMID:26901226

  13. MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.

    Science.gov (United States)

    Tek, Alex; Korostelev, Andrei A; Flores, Samuel Coulbourn

    2016-01-08

    Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.

  14. Formation of the conserved pseudouridine at position 55 in archaeal tRNA.

    Science.gov (United States)

    Roovers, Martine; Hale, Caryn; Tricot, Catherine; Terns, Michael P; Terns, Rebecca M; Grosjean, Henri; Droogmans, Louis

    2006-01-01

    Pseudouridine (Psi) located at position 55 in tRNA is a nearly universally conserved RNA modification found in all three domains of life. This modification is catalyzed by TruB in bacteria and by Pus4 in eukaryotes, but so far the Psi55 synthase has not been identified in archaea. In this work, we report the ability of two distinct pseudouridine synthases from the hyperthermophilic archaeon Pyrococcus furiosus to specifically modify U55 in tRNA in vitro. These enzymes are (pfu)Cbf5, a protein known to play a role in RNA-guided modification of rRNA, and (pfu)PsuX, a previously uncharacterized enzyme that is not a member of the TruB/Pus4/Cbf5 family of pseudouridine synthases. (pfu)PsuX is hereafter renamed (pfu)Pus10. Both enzymes specifically modify tRNA U55 in vitro but exhibit differences in substrate recognition. In addition, we find that in a heterologous in vivo system, (pfu)Pus10 efficiently complements an Escherichia coli strain deficient in the bacterial Psi55 synthase TruB. These results indicate that it is probable that (pfu)Cbf5 or (pfu)Pus10 (or both) is responsible for the introduction of pseudouridine at U55 in tRNAs in archaea. While we cannot unequivocally assign the function from our results, both possibilities represent unexpected functions of these proteins as discussed herein.

  15. The central role of tRNA in genetic code expansion.

    Science.gov (United States)

    Reynolds, Noah M; Vargas-Rodriguez, Oscar; Söll, Dieter; Crnković, Ana

    2017-03-18

    The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA.

    Science.gov (United States)

    Reiter, Nicholas J; Osterman, Amy; Torres-Larios, Alfredo; Swinger, Kerren K; Pan, Tao; Mondragón, Alfonso

    2010-12-09

    Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.

  17. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway.

    Science.gov (United States)

    Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki

    2014-01-01

    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

  18. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

    Directory of Open Access Journals (Sweden)

    Tamara Fernández-Calero

    2016-02-01

    Full Text Available Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.

  19. Optimization protein productivity of human interleukin-2 through codon usage, gene copy number and intracellular tRNA concentration in CHO cells.

    Science.gov (United States)

    Ou, Kua-Chun; Wang, Chih-Yang; Liu, Kuan-Ting; Chen, Yi-Ling; Chen, Yi-Chen; Lai, Ming-Derg; Yen, Meng-Chi

    2014-11-14

    Transfer RNA (tRNA) abundance is one of the critical factors for the enhancement of protein productivity in prokaryotic and eukaryotic hosts. Gene copy number of tRNA and tRNA codon usage bias are generally used to match tRNA abundance of protein-expressing hosts and to optimize the codons of recombinant proteins. Because sufficient concentration of intracellular tRNA and optimized codons of recombinant proteins enhanced translation efficiency, we hypothesized that sufficient supplement of host's tRNA improved protein productivity in mammalian cells. First, the small tRNA sequencing results of CHO-K1 cells showed moderate positive correlation with gene copy number and codon usage bias. Modification of human interleukin-2 (IL-2) through codons with high gene copy number and high codon usage bias (IL-2 HH, modified on Leu, Thr, Glu) significantly increased protein productivity in CHO-K1 cells. In contrast, modification through codons with relatively high gene copy number and low codon usage bias (IL-2 HL, modified on Ala, Thr, Val), or relatively low gene copy number and low codon usage bias (IL-2 LH, modified on Ala, Thr, Val) did not increase IL-2 productivity significantly. Furthermore, supplement of the alanine tRNA or threonine tRNA increased IL-2 productivity of IL-2 HL. In summary, we revealed a potential strategy to enhance productivity of recombinant proteins, which may be applied in production of protein drug or design of DNA vaccine.

  20. APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast.

    Science.gov (United States)

    Saini, Natalie; Roberts, Steven A; Sterling, Joan F; Malc, Ewa P; Mieczkowski, Piotr A; Gordenin, Dmitry A

    2017-05-01

    Variations in mutation rates across the genome have been demonstrated both in model organisms and in cancers. This phenomenon is largely driven by the damage specificity of diverse mutagens and the differences in DNA repair efficiency in given genomic contexts. Here, we demonstrate that the single-strand DNA-specific cytidine deaminase APOBEC3B (A3B) damages tRNA genes at a 1000-fold higher efficiency than other non-tRNA genomic regions in budding yeast. We found that A3B-induced lesions in tRNA genes were predominantly located on the non-transcribed strand, while no transcriptional strand bias was observed in protein coding genes. Furthermore, tRNA gene mutations were exacerbated in cells where RNaseH expression was completely abolished (Δrnh1Δrnh35). These data suggest a transcription-dependent mechanism for A3B-induced tRNA gene hypermutation. Interestingly, in strains proficient in DNA repair, only 1% of the abasic sites formed upon excision of A3B-deaminated cytosines were not repaired leading to mutations in tRNA genes, while 18% of these lesions failed to be repaired in the remainder of the genome. A3B-induced mutagenesis in tRNA genes was found to be efficiently suppressed by the redundant activities of both base excision repair (BER) and the error-free DNA damage bypass pathway. On the other hand, deficiencies in BER did not have a profound effect on A3B-induced mutations in CAN1, the reporter for protein coding genes. We hypothesize that differences in the mechanisms underlying ssDNA formation at tRNA genes and other genomic loci are the key determinants of the choice of the repair pathways and consequently the efficiency of DNA damage repair in these regions. Overall, our results indicate that tRNA genes are highly susceptible to ssDNA-specific DNA damaging agents. However, increased DNA repair efficacy in tRNA genes can prevent their hypermutation and maintain both genome and proteome homeostasis. Published by Elsevier B.V.

  1. Regulatory requirements for providing adequate veterinary care to research animals.

    Science.gov (United States)

    Pinson, David M

    2013-09-01

    Provision of adequate veterinary care is a required component of animal care and use programs in the United States. Program participants other than veterinarians, including non-medically trained research personnel and technicians, also provide veterinary care to animals, and administrators are responsible for assuring compliance with federal mandates regarding adequate veterinary care. All program participants therefore should understand the regulatory requirements for providing such care. The author provides a training primer on the US regulatory requirements for the provision of veterinary care to research animals. Understanding the legal basis and conditions of a program of veterinary care will help program participants to meet the requirements advanced in the laws and policies.

  2. A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α

    Science.gov (United States)

    Begley, Ulrike; Sosa, Maria Soledad; Avivar-Valderas, Alvaro; Patil, Ashish; Endres, Lauren; Estrada, Yeriel; Chan, Clement TY; Su, Dan; Dedon, Peter C; Aguirre-Ghiso, Julio A; Begley, Thomas

    2013-01-01

    Emerging evidence points to aberrant regulation of translation as a driver of cell transformation in cancer. Given the direct control of translation by tRNA modifications, tRNA modifying enzymes may function as regulators of cancer progression. Here, we show that a tRNA methyltransferase 9-like (hTRM9L/KIAA1456) mRNA is down-regulated in breast, bladder, colorectal, cervix and testicular carcinomas. In the aggressive SW620 and HCT116 colon carcinoma cell lines, hTRM9L is silenced and its re-expression and methyltransferase activity dramatically suppressed tumour growth in vivo. This growth inhibition was linked to decreased proliferation, senescence-like G0/G1-arrest and up-regulation of the RB interacting protein LIN9. Additionally, SW620 cells re-expressing hTRM9L did not respond to hypoxia via HIF1-α-dependent induction of GLUT1. Importantly, hTRM9L-negative tumours were highly sensitive to aminoglycoside antibiotics and this was associated with altered tRNA modification levels compared to antibiotic resistant hTRM9L-expressing SW620 cells. Our study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-α-dependent mechanisms. It also suggests that aminoglycoside antibiotics may be useful to treat hTRM9L-deficient tumours. PMID:23381944

  3. Selenium biofortification in radish enhances nutritional quality via accumulation of methyl-selenocysteine and promotion of transcripts and metabolites related to glucosinolates, phenolics and amino acids

    Directory of Open Access Journals (Sweden)

    Michela Schiavon

    2016-09-01

    metabolized selenate to the anticarcinogenic compound Se-methyl-selenocysteine. Selenate treatment enhanced levels of other nutraceuticals in radish roots, including glucoraphanin. Therefore, Se biofortification can produce plants with superior health benefits.

  4. Selenium Biofortification in Radish Enhances Nutritional Quality via Accumulation of Methyl-Selenocysteine and Promotion of Transcripts and Metabolites Related to Glucosinolates, Phenolics, and Amino Acids

    Science.gov (United States)

    Schiavon, Michela; Berto, Chiara; Malagoli, Mario; Trentin, Annarita; Sambo, Paolo; Dall'Acqua, Stefano; Pilon-Smits, Elizabeth A. H.

    2016-01-01

    selenate to the anticarcinogenic compound Se-methyl-selenocysteine. Selenate treatment enhanced levels of other nutraceuticals in radish roots, including glucoraphanin. Therefore, Se biofortification can produce plants with superior health benefits. PMID:27683583

  5. Effects of Combinatorial Expression of selA, selB and selC Genes on the Efficiency of Selenocysteine Incorporation in Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    XU Ya-wei; YAN Gang-lin; LUO Gui-min; JIANG Zhi-hua; MU Ying; ZHANG Lei; ZHAO Si-qi; LIU Shu-jun; WANG Cheng; ZHAO Yang; L(U) Shao-wu

    2013-01-01

    In Escherichia coli,four gene products(selA,selB,selC and selD) and a selenocysteine(Sec) insertion sequence(SECIS) are required for the correct translation of UGA codons encoding Sec.Previous studies have shown that the stoichiometry of selenoproteine mRNA and elongation factor SelB affect the efficiency of Sec incorporation.Herein lies a detailed analysis of the effects of co-expressing selA,selB and selC genes under inducible promoters on the incorporation efficiency of Sec.Over-expression of either selA or selB reduced the efficiency of Sec incorporation by 61.1% or 11.6%,respectively,compared to the over-expression of the reporter vector alone did.Concomitant over-expression of selC with selA or selB completely reversed the reduce of the efficiency of Sec but still reduced the efficiency of the incorporation relative to that observed for expression of selC alone.Over-expression of selC gene alone under L-arabinose induction reduced the efficiency of the incorporation relative to that observed for co-expressing selC with selA and selB under the control of its endogenous promoter in the absence of L-arabinose.Co-expression of selA,selB and selC with selA or selB under the control of inducible promoters increased the efficiency of Sec incorporation by 69.7%.Moreover,inducing selenoprotein-related gene expression during the late exponential phase increased the efficiency of Sec incorporation by a factor of 5.4 relative to that observed for the reporter vector alone.These results suggest that the co-expression of selA,selB and selC in Escherichia coli under the control of inducible promoters is a viable and promising strategy for increasing the yields of selenoproteins.

  6. Selenium Biofortification in Radish Enhances Nutritional Quality via Accumulation of Methyl-Selenocysteine and Promotion of Transcripts and Metabolites Related to Glucosinolates, Phenolics, and Amino Acids.

    Science.gov (United States)

    Schiavon, Michela; Berto, Chiara; Malagoli, Mario; Trentin, Annarita; Sambo, Paolo; Dall'Acqua, Stefano; Pilon-Smits, Elizabeth A H

    2016-01-01

    the anticarcinogenic compound Se-methyl-selenocysteine. Selenate treatment enhanced levels of other nutraceuticals in radish roots, including glucoraphanin. Therefore, Se biofortification can produce plants with superior health benefits.

  7. What is an Adequate Standard of Living During Retirement?

    NARCIS (Netherlands)

    Binswanger, J.; Schunk, D.

    2008-01-01

    Many economists and policy-makers argue that households do not save enough to maintain an adequate standard of living during retirement. However, there is no consensus on the answer to the underlying question what this standard should be, despite the fact that it is crucial for the design of saving

  8. Quasi-Type δ Semigroups with an Adequate Transversal

    Institute of Scientific and Technical Information of China (English)

    Shou Feng WANG

    2011-01-01

    In this paper,some properties of quasi-type δ semigroups with an adequate transversal are explored.In particular,abundant semigroups with a cancellative transversal are characterized.Our results generalize and enrich Saito's results on quasi-orthodox semigroups with an inverse transversal.

  9. Is the Stock of VET Skills Adequate? Assessment Methodologies.

    Science.gov (United States)

    Blandy, Richard; Freeland, Brett

    In Australia and elsewhere, four approaches have been used to determine whether stocks of vocational education and training (VET) skills are adequate to meet industry needs. The four methods are as follows: (1) the manpower requirements approach; (2) the international, national, and industry comparisons approach; (3) the labor market analysis…

  10. Do Beginning Teachers Receive Adequate Support from Their Headteachers?

    Science.gov (United States)

    Menon, Maria Eliophotou

    2012-01-01

    The article examines the problems faced by beginning teachers in Cyprus and the extent to which headteachers are considered to provide adequate guidance and support to them. Data were collected through interviews with 25 school teachers in Cyprus, who had recently entered teaching (within 1-5 years) in public primary schools. According to the…

  11. 4 CFR 200.14 - Responsibility for maintaining adequate safeguards.

    Science.gov (United States)

    2010-01-01

    ... identifiable personal data and automated systems shall be adequately trained in the security and privacy of... records in which identifiable personal data are processed or maintained, including all reports and output... personal records or data; must minimize, to the extent practicable, the risk that skilled technicians...

  12. N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network.

    Science.gov (United States)

    Tomikawa, Chie; Yokogawa, Takashi; Kanai, Tamotsu; Hori, Hiroyuki

    2010-01-01

    N(7)-methylguanine at position 46 (m(7)G46) in tRNA is produced by tRNA (m(7)G46) methyltransferase (TrmB). To clarify the role of this modification, we made a trmB gene disruptant (DeltatrmB) of Thermus thermophilus, an extreme thermophilic eubacterium. The absence of TrmB activity in cell extract from the DeltatrmB strain and the lack of the m(7)G46 modification in tRNA(Phe) were confirmed by enzyme assay, nucleoside analysis and RNA sequencing. When the DeltatrmB strain was cultured at high temperatures, several modified nucleotides in tRNA were hypo-modified in addition to the lack of the m(7)G46 modification. Assays with tRNA modification enzymes revealed hypo-modifications of Gm18 and m(1)G37, suggesting that the m(7)G46 positively affects their formations. Although the lack of the m(7)G46 modification and the hypo-modifications do not affect the Phe charging activity of tRNA(Phe), they cause a decrease in melting temperature of class I tRNA and degradation of tRNA(Phe) and tRNA(Ile). (35)S-Met incorporation into proteins revealed that protein synthesis in DeltatrmB cells is depressed above 70 degrees C. At 80 degrees C, the DeltatrmB strain exhibits a severe growth defect. Thus, the m(7)G46 modification is required for cell viability at high temperatures via a tRNA modification network, in which the m(7)G46 modification supports introduction of other modifications.

  13. Optical Kerr effect of tRNA solution induced by femtosecond laser pulses

    Science.gov (United States)

    Kucia, Weronika E.; Sharma, Gargi; Joseph, Cecil S.; Sarbak, Szymon; Oliver, Cameron; Dobek, Andrzej; Giles, Robert H.

    2016-10-01

    The optical Kerr effect (OKE) in a transfer ribonucleic acid (tRNA) solution induced by femtosecond pulses of linearly polarized pump light (λi = 800 nm) and sounded by probe light (λp = 800 nm) was studied. The measurements were performed to find nonlinear optical parameters describing a single molecule (molecular Kerr constant K, mean nonlinear third order optical polarizability cpi) and to compare them with our previous OKE results obtained in ns and ps time range. The OKE experiment has proven to be an efficient method to obtain the nonlinear parameters of single molecules in solution, which reflects dynamic structure changes.

  14. Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

    Science.gov (United States)

    van der Gulik, Peter T. S.; Hoff, Wouter D.

    2016-01-01

    Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA. PMID:27454314

  15. RNA polymerase II induced transcription of tRNA genes and processing of the mRNAs in yeast

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Only 5'-halves were produced when the terminator sequence for RNA polymerase (pol) 1II transcrip-tion was inserted into the intron of yeast tRNATyr gene. If a promoter and a terminator for pol II transcription flanked it,the tRNA gene could be transcribed by pol II, but the transcripts could not be processed into mature tRNAs. In con-trast, tRNA gene could also be transcribed by pol III and the transcripts could be processed into mature tRNAs even if a promoter and a terminator for pol II transcription flanked it. Pol II transcripts, modified with a self-cleaved hannner-head structure at 3'-end, were processed into mature tRNAs in the medium containing 100 mmol/L Mg2+ , indicating that the 3'-long trailer sequence blocks the maturation of tRNA gene transcripts by pol II.

  16. Movement of the 3'-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

    DEFF Research Database (Denmark)

    Kirillov, Stanislav; Porse, Bo Torben; Vester, Birthe;

    1997-01-01

    Determining how antibiotics inhibit ribosomal activity requires a detailed understanding of the interactions and relative movement of tRNA, mRNA and the ribosome. Recent models for the formation of hybrid tRNA binding sites during the elongation cycle have provided a basis for re-evaluating earlier......RNA-ribosome binding. Nevertheless, these relatively weak interactions determine the unidirectional movement of tRNAs through the ribosome and, moreover, they appear to be particularly susceptible to perturbation by antibiotics. Here we summarise current ideas relating particularly to the movement of the 3'-ends of t......RNA through the ribosome and consider possible inhibitory mechanisms of the peptidyl transferase antibiotics....

  17. La adaptación a la deficiencia de zinc en cianobacterias. Papel de treonil-trna sintetasas duplicadas

    OpenAIRE

    2016-01-01

    Falta palabras claves Las aminoacil tRNA sintetasas (aaRSs) son las enzimas que catalizan la carga del aminoácido en el tRNA y son las responsables de mantener la fidelidad en la traducción del código genético. Las aaRSs son componentes esenciales de la síntesis proteica y son ubicuas en todos los dominios de la vida (Ibba y Sol, 2000; Perona y Hadd, 2012). La cianobacteria filamentosa Anabaena sp.PCC 7120 contiene dos genes de treonil tRNA sintetasa, alr0335(thrS1) y all4723 (thrS2), ...

  18. Structure and Activity of an Aminoacyl-tRNA Synthetase that Charges tRNA with Nitro-Tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Buddha,M.; Crane, B.

    2005-01-01

    The most divergent of two tryptophanyl tRNA synthetases (TrpRS II) found in Deinococcus radiodurans interacts with a nitric oxide synthase protein that produces 4-nitro-tryptophan (4-NRP). TrpRS II efficiently charges transfer RNATrp with 4-NRP and 5-hydroxy-tryptophan (5-HRP). The crystal structures of TrpRS II bound to tryptophan and 5-HRP reveal residue substitutions that accommodate modified indoles. A class of auxiliary bacterial TrpRSs conserve this capacity to charge tRNA with nonstandard amino acids.

  19. The Complexity of Recognition of Linguistically Adequate Dependency Grammars

    CERN Document Server

    Neuhaus, P; Neuhaus, Peter; Broeker, Norbert

    1997-01-01

    Results of computational complexity exist for a wide range of phrase structure-based grammar formalisms, while there is an apparent lack of such results for dependency-based formalisms. We here adapt a result on the complexity of ID/LP-grammars to the dependency framework. Contrary to previous studies on heavily restricted dependency grammars, we prove that recognition (and thus, parsing) of linguistically adequate dependency grammars is NP-complete.

  20. Arabidopsis: an adequate model for dicot root systems?

    OpenAIRE

    Zobel, Richard W.

    2016-01-01

    The Arabidopsis root system is frequently considered to have only three classes of root: primary, lateral, and adventitious. Research with other plant species has suggested up to 8 different developmental/functional classes of root for a given plant root system. If Arabidopsis has only three classes of root, it may not be an adequate model for eudicot plant root systems. Recent research, however, can be interpreted to suggest that pre-flowering Arabidopsis does have at least five (5) of th...

  1. Arabidopsis: An Adequate Model for Dicot Root Systems?

    OpenAIRE

    Zobel, Richard W.

    2016-01-01

    The Arabidopsis root system is frequently considered to have only three classes of root: primary, lateral, and adventitious. Research with other plant species has suggested up to eight different developmental/functional classes of root for a given plant root system. If Arabidopsis has only three classes of root, it may not be an adequate model for eudicot plant root systems. Recent research, however, can be interpreted to suggest that pre-flowering Arabidopsis does have at least five (5) of t...

  2. Undergraduate UK nutrition education might not adequately address weight management

    OpenAIRE

    Rogerson, David; Soltani, Hora; Copeland, Robert

    2015-01-01

    Objective: Weight management appears to be multidimensional and complex, and registered nutritionists might work to educate, promote and provide weight-management services to communities, groups and individuals. However, nutrition education might not adequately reflect the weight-management requirements of individuals and groups. The aim of the present study was to investigate if the Association for Nutrition’s undergraduate core competency framework for accredited Nutrition degrees sufficien...

  3. From End to End: tRNA Editing at 5'- and 3'-Terminal Positions

    Science.gov (United States)

    Betat, Heike; Long, Yicheng; Jackman, Jane E.; Mörl, Mario

    2014-01-01

    During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems. PMID:25535083

  4. From End to End: tRNA Editing at 5'- and 3'-Terminal Positions

    Directory of Open Access Journals (Sweden)

    Heike Betat

    2014-12-01

    Full Text Available During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems.

  5. Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability

    Science.gov (United States)

    2015-01-01

    Folding dynamics are ubiquitously involved in controlling the multivariate functions of RNAs. While the high thermodynamic stabilities of some RNAs favor purely native states at equilibrium, it is unclear whether weakly stable RNAs exist in random, partially folded states or sample well-defined, globally folded conformations. Using a folding assay that precisely tracks the formation of native aminoacylable tRNA, we show that the folding of a weakly stable human mitochondrial (hmt) leucine tRNA is hierarchical with a distinct kinetic folding intermediate. The stabilities of the native and intermediate conformers are separated by only about 1.2 kcal/mol, and the species are readily interconvertible. Comparison of folding dynamics between unmodified and fully modified tRNAs reveals that post-transcriptional modifications produce a more constrained native structure that does not sample intermediate conformations. These structural dynamics may thus be crucial for recognition by some modifying enzymes in vivo, especially those targeting the globular core region, by allowing access to pretransition state conformers. Reduced conformational sampling of the native, modified tRNAs could then permit improved performance in downstream processes of translation. More generally, weak stabilities of small RNAs that fold in the absence of chaperone proteins may facilitate conformational switching that is central to biological function. PMID:24520994

  6. SYNTHESIS AND DETERMINATION OF THE BIOLOGICAL ACTIVITIES OF YEAST ALANINE tRNA ANALOGUES

    Institute of Scientific and Technical Information of China (English)

    刘建华; 王德宝

    1991-01-01

    The role of base modification in yeast tRNAAl(?) function in protein synthesis was examined by the use of unmodified tRNA analogues. Unmodified full length tRNAs, 5’-half tRNAs (nucleotides 1-35) and 3’-half tRNAs (nucleotides 37-75) were transcribed in vitro using T7-RNA polymerase. Unmodified tRNA half molecules were joined to normally modified half molecules (5’-half, nucleotides 1-36; 3’-half, nucleotides 36-75) by T4-RNA ligase. Using this method, we synthesized three analogues of yeast tRNAAl(?): (i) tRNAAl(?) which lacks base modifications in the 5’-half of the molecule; (ii) tRNAAl(?) which lacks base modifications in the 3’-half of the molecule; and (iii) tRNAAla completely lacking base modifications. We determined the biological activities of these analogues. In rat aminoacyl-tRNA synthetase reactions, the alanine acceptance activity decreased by 52%, 79% and 85% when modified bases were absent from the 5’-half molecule, the 3’-half molecule or the total molecule, respectively. In rabbit retic

  7. Mutations induced by monofunctional and bifunctional phosphoramide mustards in supF tRNA gene.

    Science.gov (United States)

    Mudipalli, A; Maccubbin, A E; Nadadur, S S; Struck, R F; Gurtoo, H L

    1997-11-19

    The relative mutagenicity, nature of the mutations and the sequence specificity of mutations induced by the bifunctional alkylating agent, phosphoramide mustard (PM) and a monofunctional derivative, dechloroethyl phosphoramide mustard (dePM), were analyzed by the Ames test and by an in vitro shuttle vector mutagenesis assay. Both PM and dePM increased the mutation frequency above background in either assay. However, on an equimolar basis, dePM was less mutagenic than PM. In the in vitro shuttle vector mutagenesis assay, sequencing demonstrated that about 40% of the mutant plasmids contained more than one mutation in the supF tRNA gene segment of the plasmid. About 70% of the mutations observed in dePM-treated plasmids were single base substitutions with A:T and G:C base pairs being mutated at equivalent rates. In contrast, only about 50% of the mutations observed in PM-treated plasmids were single base substitutions, 80% of which involved G:C base pairs. Single base deletions and insertions were found in approximately equal proportions with both compounds; however, these lesions were in greater abundance in PM-treated plasmids. Putative hot-spots for mutation in the supF tRNA gene included base pairs at position 102 and 110 for PM and positions 170 and 171 for dePM.

  8. Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

    Science.gov (United States)

    Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

    2015-06-18

    Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development.

  9. Genetic modification of preimplantation embryos: toward adequate human research policies.

    Science.gov (United States)

    Dresser, Rebecca

    2004-01-01

    Citing advances in transgenic animal research and setbacks in human trials of somatic cell genetic interventions, some scientists and others want to begin planning for research involving the genetic modification of human embryos. Because this form of genetic modification could affect later-born children and their offspring, the protection of human subjects should be a priority in decisions about whether to proceed with such research. Yet because of gaps in existing federal policies, embryo modification proposals might not receive adequate scientific and ethical scrutiny. This article describes current policy shortcomings and recommends policy actions designed to ensure that the investigational genetic modification of embryos meets accepted standards for research on human subjects.

  10. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    NARCIS (Netherlands)

    L.M. 't Hart (Leen); H.A.P. Pols (Huib); T. Hansen (Torben); I. Rietveld (Ingrid); J.M. Dekker (Jacqueline); J.A. Maassen (Johannes); M.G.A.A.M. Nijpels (Giel); G.M.C. Janssen (George); P.P. Arp (Pascal); R.J. Heine (Robert); A.G. Uitterlinden (André); T. Jorgensen (Torben); C.M. van Duijn (Cock); K. Borch-Johnsen; O. Pedersen (Oluf)

    2005-01-01

    textabstractPreviously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA s

  11. Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

    NARCIS (Netherlands)

    Fairley, Jennifer A.; Mitchell, Louise E.; Berg, Tracy; Kenneth, Niall S.; von Schubert, Conrad; Sillje, Herman H. W.; Medema, Rene H.; Nigg, Erich A.; White, Robert J.

    2012-01-01

    Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase Ill (pol Ill) through direct binding and phosphorylation of transcription factor Brit During interphase, Plk1 promotes

  12. An entropy based analysis of the relationship between the DOW JONES Index and the TRNA Sentiment series

    NARCIS (Netherlands)

    D.E. Allen (David); M.J. McAleer (Michael); A.K. Singh (Abhay)

    2016-01-01

    textabstractThis paper features an analysis of the relationship between the DOW JONES Industrial Average Index (DJIA) and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA)1 provided by SIRCA (The Securities Industry Research Centre of the Asia Pacic). T

  13. Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas.

    Science.gov (United States)

    Salinas, Thalia; Duby, Francéline; Larosa, Véronique; Coosemans, Nadine; Bonnefoy, Nathalie; Motte, Patrick; Maréchal-Drouard, Laurence; Remacle, Claire

    2012-09-01

    Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery.

  14. Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

    NARCIS (Netherlands)

    Fairley, Jennifer A.; Mitchell, Louise E.; Berg, Tracy; Kenneth, Niall S.; von Schubert, Conrad; Sillje, Herman H. W.; Medema, Rene H.; Nigg, Erich A.; White, Robert J.

    2012-01-01

    Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase Ill (pol Ill) through direct binding and phosphorylation of transcription factor Brit During interphase, Plk1 promotes

  15. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    DEFF Research Database (Denmark)

    hart, Leen M; Hansen, Torben; Rietveld, Ingrid

    2005-01-01

    Previously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA synthetase...

  16. Adequate sizing and motor exploitation: Motor energy management

    Directory of Open Access Journals (Sweden)

    Kostić Miloje M.

    2011-01-01

    Full Text Available Motor energy management includes adequate sizing, control and improvement of electric energy quality, i.e. voltage quality (reducing voltage unbalance and harmonics distortion, and the proper maintenance. The specific motor price per kW is approximately constant for motors rated from 5 kW to 20 kW. By adequate sizing, or by proper replacement of the old motor with the new one, with rated output power reduced by 20% to 50% the smaller motor will be also cheaper by 20% to 50%. When the 22 kW motor is replaced with the new 15 kW that costs 64% of the price of a new 22 kW motor, the efficiency is increased by 3.6% (Example in paper. On the basis of our investigation results, it is confirmed that there are significant possibilities for energy savings by setting voltage values within the ±5% voltage band (Un±5%, since more than 80% induction motors are under loaded (£70%, especially small and medium rated power (1-30 kW motors.

  17. Barriers to adequate prenatal care utilization in American Samoa.

    Science.gov (United States)

    Hawley, Nicola L; Brown, Carolyn; Nu'usolia, Ofeira; Ah-Ching, John; Muasau-Howard, Bethel; McGarvey, Stephen T

    2014-12-01

    The objective of this study is to describe the utilization of prenatal care in American Samoan women and to identify socio-demographic predictors of inadequate prenatal care utilization. Using data from prenatal clinic records, women (n = 692) were categorized according to the adequacy of prenatal care utilization index as having received adequate plus, adequate, intermediate or inadequate prenatal care during their pregnancy. Categorical socio-demographic predictors of the timing of initiation of prenatal care (week of gestation) and the adequacy of received services were identified using one way analysis of variance and independent samples t tests. Between 2001 and 2008 85.4 % of women received inadequate prenatal care. Parity (P = 0.02), maternal unemployment (P = 0.03), and both parents being unemployed (P = 0.03) were negatively associated with the timing of prenatal care initiation. Giving birth in 2007-2008, after a prenatal care incentive scheme had been introduced in the major hospital, was associated with earlier initiation of prenatal care (20.75 vs. 25.12 weeks; P prenatal care utilization in American Samoa is a major concern. Improving healthcare accessibility will be key in encouraging women to attend prenatal care. The significant improvements in the adequacy of prenatal care seen in 2007-2008 suggest that the prenatal care incentive program implemented in 2006 may be a very positive step toward addressing issues of prenatal care utilization in this population.

  18. Is prophetic discourse adequate to address global economic justice?

    Directory of Open Access Journals (Sweden)

    Piet J. Naudé

    2011-06-01

    Full Text Available This article outlined key features of prophetic discourse and investigated whether this form of moral discourse adequately addresses issues of economic injustice. It is shown that the strength of prophetic discourse is its ability to denounce instances of injustice whilst at the same time announcing a God-willed alternative future. The ‘preferential option for the poor’ in Latin American liberation theologies is treated as a case study of the influence of prophetic discourse in contexts of perceived economic injustice. Also the core weaknesses of prophetic discourse are investigated, specifically its incomplete moral argument, weak moral analyses, silence on transition measures, and its inability to take a positive stance on reforms in the system from which itself benefits. In the final section it is concluded that prophetic discourse plays an indispensable role in addressing issues of global economic justice, but – taken by itself – it is not an adequate form of moral discourse to address concrete matters of justice.

  19. Quantifying dose to the reconstructed breast: Can we adequately treat?

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Eugene; Marsh, Robin B.; Griffith, Kent A.; Moran, Jean M. [Department of Radiation Oncology, University of Michigan, Ann Arbor, MI (United States); Pierce, Lori J., E-mail: ljpierce@umich.edu [Department of Radiation Oncology, University of Michigan, Ann Arbor, MI (United States)

    2013-04-01

    To evaluate how immediate reconstruction (IR) impacts postmastectomy radiotherapy (PMRT) dose distributions to the reconstructed breast (RB), internal mammary nodes (IMN), heart, and lungs using quantifiable dosimetric end points. 3D conformal plans were developed for 20 IR patients, 10 autologous reconstruction (AR), and 10 expander-implant (EI) reconstruction. For each reconstruction type, 5 right- and 5 left-sided reconstructions were selected. Two plans were created for each patient, 1 with RB coverage alone and 1 with RB + IMN coverage. Left-sided EI plans without IMN coverage had higher heart Dmean than left-sided AR plans (2.97 and 0.84 Gy, p = 0.03). Otherwise, results did not vary by reconstruction type and all remaining metrics were evaluated using a combined AR and EI dataset. RB coverage was adequate regardless of laterality or IMN coverage (Dmean 50.61 Gy, D95 45.76 Gy). When included, IMN Dmean and D95 were 49.57 and 40.96 Gy, respectively. Mean heart doses increased with left-sided treatment plans and IMN inclusion. Right-sided treatment plans and IMN inclusion increased mean lung V{sub 20}. Using standard field arrangements and 3D planning, we observed excellent coverage of the RB and IMN, regardless of laterality or reconstruction type. Our results demonstrate that adequate doses can be delivered to the RB with or without IMN coverage.

  20. Barriers to adequate prenatal care utilization in American Samoa

    Science.gov (United States)

    Hawley, Nicola L; Brown, Carolyn; Nu’usolia, Ofeira; Ah-Ching, John; Muasau-Howard, Bethel; McGarvey, Stephen T

    2013-01-01

    Objective To describe the utilization of prenatal care in American Samoan women and to identify socio-demographic predictors of inadequate prenatal care utilization. Methods Using data from prenatal clinic records, women (n=692) were categorized according to the Adequacy of Prenatal Care Utilization Index as having received adequate plus, adequate, intermediate or inadequate prenatal care during their pregnancy. Categorical socio-demographic predictors of the timing of initiation of prenatal care (week of gestation) and the adequacy of received services were identified using one way Analysis of Variance (ANOVA) and independent samples t-tests. Results Between 2001 and 2008 85.4% of women received inadequate prenatal care. Parity (P=0.02), maternal unemployment (P=0.03), and both parents being unemployed (P=0.03) were negatively associated with the timing of prenatal care initation. Giving birth in 2007–2008, after a prenatal care incentive scheme had been introduced in the major hospital, was associated with earlier initiation of prenatal care (20.75 versus 25.12 weeks; Pprenatal care utilization in American Samoa is a major concern. Improving healthcare accessibility will be key in encouraging women to attend prenatal care. The significant improvements in the adequacy of prenatal care seen in 2007–2008 suggest that the prenatal care incentive program implemented in 2006 may be a very positive step toward addressing issues of prenatal care utilization in this population. PMID:24045912

  1. Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code

    DEFF Research Database (Denmark)

    Yadavalli, Srujana S; Ibba, Michael

    2013-01-01

    Mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer RNA (tRNA) pairs by aminoacyl-tRNA synthetases (aaRSs) and inaccurate selection of aminoacyl-tRNAs by the ribosome. Many aaRSs actively edit non-cognate amino acids, but editing mechanisms...... are not evolutionarily conserved, and their physiological significance remains unclear. To address the connection between aaRSs and mistranslation, the evolutionary divergence of tyrosine editing by phenylalanyl-tRNA synthetase (PheRS) was used as a model. Certain PheRSs are naturally error prone, most notably...... a Mycoplasma example that displayed a low level of specificity consistent with elevated mistranslation of the proteome. Mycoplasma PheRS was found to lack canonical editing activity, relying instead on discrimination against the non-cognate amino acid by kinetic proofreading. This mechanism of discrimination...

  2. Natural aminoacyl tRNA synthetase fragment enhances cardiac function after myocardial infarction.

    Directory of Open Access Journals (Sweden)

    Margaret E McCormick

    Full Text Available A naturally-occurring fragment of tyrosyl-tRNA synthetase (TyrRS has been shown in higher eukaryotes to 'moonlight' as a pro-angiogenic cytokine in addition to its primary role in protein translation. Pro-angiogenic cytokines have previously been proposed to be promising therapeutic mechanisms for the treatment of myocardial infarction. Here, we show that systemic delivery of the natural fragment of TyRS, mini-TyrRS, improves heart function in mice after myocardial infarction. This improvement is associated with reduced formation of scar tissue, increased angiogenesis of cardiac capillaries, recruitment of c-kitpos cells and proliferation of myocardial fibroblasts. This work demonstrates that mini-TyrRS has beneficial effects on cardiac repair and regeneration and offers support for the notion that elucidation of the ever expanding repertoire of noncanonical functions of aminoacyl tRNA synthetases offers unique opportunities for development of novel therapeutics.

  3. Limited diagnostic value of enzyme analysis in patients with mitochondrial tRNA mutations

    DEFF Research Database (Denmark)

    Wibrand, Flemming; Jeppesen, Tina Dysgaard; Frederiksen, Anja L

    2010-01-01

    We evaluated the diagnostic value of respiratory chain (RC) enzyme analysis of muscle in adult patients with mitochondrial myopathy (MM). RC enzyme activity was measured in muscle biopsies from 39 patients who carry either the 3243A>G mutation, other tRNA point mutations, or single, large....... Only 10% of patients with the 3243A>G point mutation had decreased enzyme activity of one or more RC complexes, whereas this was the case for 83% of patients with other point mutations and 62% of patients with deletions. Abnormal muscle histochemistry was found in 65%, 100%, and 85% of patients......-scale deletions of mtDNA. Findings were compared with those obtained from asymptomatic relatives with the 3243A>G mutation, myotonic dystrophy patients, and healthy subjects. Plasma lactate concentration, maximal oxygen uptake, and ragged-red fibers/cytochrome c-negative fibers in muscle were also determined...

  4. On origin of genetic code and tRNA before translation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs

    2011-02-01

    Full Text Available Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas. A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1 the fundamental veto on "foresight evolution", 2 modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3 the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code the anticodon(2-3/codon(1-2 tetramers to their anticodon(1-2/codon(2-3 counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator to the eventual 76 base

  5. The nucleotide sequence of histidine tRNA gamma of Drosophila melanogaster.

    OpenAIRE

    Altwegg, M; Kubli, E

    1980-01-01

    The nucleotide sequence of D. melanogaster histidine tRNA gamma was determined to be: pG-G-C-C-G-U-G-A-U-C-G-U-C-psi-A-G-D-G-G-D-D-A-G-G-A-C-C-C-C-A-C-G-psi-U-G-U-G- m1G-C-C-G-U-G-G-U-A-A-C-C-m5C-A-G-G-U-psi-C-G-m1A-A-U-C-C-U-G-G-U-C-A-C-G-G-m5C -A-C-C-AOH. An additional unpaired G is found at the 5' end, and the T in the TpsiC loop is replaced by a U.

  6. Insertion near the mitochondrial tyrosine tRNA gene in patients with mitochondrial diseases

    Energy Technology Data Exchange (ETDEWEB)

    Goto, Y.; Nonaka, I. [National Institute of Neuroscience, Tokyo (Japan); Horai, S. [National Institute of Genetics, Mishima (Japan)

    1994-09-01

    The 3243 mutation commonly found in patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) has been occasionally detected in patients with chronic progressive external opthalmoplegia (CPEO). To elucidate the molecular mechanism underlying this phenomenon, an extensive mitochondrial (mt) DNA study was performed on such a patient (3243-CPEO). The newly discovered insertion was located in the noncoding region between cytrochrome c oxidase subunit 1 and tyrosine tRNA. The insertion was not found in 58 or 22 CPEO patients with or without mtDNA large-scale deletion but in another 3243-CPEO patient. In addition, the insertion was present in 1 of 116 normal Japanese, who had no 3243 mutation, and in 3 of 68 3243-MELAS patients. These results raise the possibility that the phenotypic expression of the 3243 mutation could be modulated or arranged by additional mtDNA mutations.

  7. tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World

    Directory of Open Access Journals (Sweden)

    Savio T. de Farias

    2016-03-01

    Full Text Available Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA and the peptidyl transferase center (rRNA, proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes then arose in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by three kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA.

  8. Formation of tRNA granules in the nucleus of heat-induced human cells

    Energy Technology Data Exchange (ETDEWEB)

    Miyagawa, Ryu [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan); Mizuno, Rie [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Watanabe, Kazunori, E-mail: watanabe@ric.u-tokyo.ac.jp [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Ijiri, Kenichi [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan)

    2012-02-03

    Highlights: Black-Right-Pointing-Pointer tRNAs are tranlocated into the nucleus in heat-induced HeLa cells. Black-Right-Pointing-Pointer tRNAs form the unique granules in the nucleus. Black-Right-Pointing-Pointer tRNA ganules overlap with nuclear stress granules. -- Abstract: The stress response, which can trigger various physiological phenomena, is important for living organisms. For instance, a number of stress-induced granules such as P-body and stress granule have been identified. These granules are formed in the cytoplasm under stress conditions and are associated with translational inhibition and mRNA decay. In the nucleus, there is a focus named nuclear stress body (nSB) that distinguishes these structures from cytoplasmic stress granules. Many splicing factors and long non-coding RNA species localize in nSBs as a result of stress. Indeed, tRNAs respond to several kinds of stress such as heat, oxidation or starvation. Although nuclear accumulation of tRNAs occurs in starved Saccharomyces cerevisiae, this phenomenon is not found in mammalian cells. We observed that initiator tRNA{sup Met} (Meti) is actively translocated into the nucleus of human cells under heat stress. During this study, we identified unique granules of Meti that overlapped with nSBs. Similarly, elongator tRNA{sup Met} was translocated into the nucleus and formed granules during heat stress. Formation of tRNA granules is closely related to the translocation ratio. Then, all tRNAs may form the specific granules.

  9. Chromatographic evidence that the AAA-coding isoacceptor of lysine tRNA primes DNA synthesis in murine mammary tumor virus

    Energy Technology Data Exchange (ETDEWEB)

    Waters, L.C.

    1981-07-30

    Most of the tRNA encapsulated within the murine mammary tumor virus is tRNA/sup LYS/. The reversed-phase chromatographic pattern of tRNA/sup LYS/ isoacceptors in the viral free tRNA and in the 70 S-associated tRNA that is released at 65/sup 0/ is similar to the pattern in virus-producing cells. However, the more tightly bound 70 S-associated tRNA/sup LYS/ is significantly enriched in the AAA-coding isoacceptor. This isoacceptor, but not the AAG-coding one, primes MuMTV 35 S RNA-directed DNA synthesis in vitro.

  10. Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral.

    Science.gov (United States)

    Dowton, Mark; Cameron, Stephen L; Dowavic, Jessica I; Austin, Andy D; Whiting, Michael F

    2009-07-01

    We present entire sequences of two hymenopteran mitochondrial genomes and the major portion of three others. We combined these data with nine previously sequenced hymenopteran mitochondrial genomes. This allowed us to infer and analyze the evolution of the 67 mitochondrial gene rearrangements so far found in this order. All of these involve tRNA genes, whereas four also involve larger (protein-coding or ribosomal RNA) genes. We find that the vast majority of mitochondrial gene rearrangements are independently derived. A maximum of four of these rearrangements represent shared, derived organizations, whereas three are convergently derived. The remaining mitochondrial gene rearrangements represent new mitochondrial genome organizations. These data are consistent with the proposal that there are an enormous number of alternative mitochondrial genome organizations possible and that mitochondrial genome organization is, for the most part, selectively neutral. Nevertheless, some mitochondrial genes appear less mobile than others. Genes close to the noncoding region are generally more mobile but only marginally so. Some mitochondrial genes rearrange in a pattern consistent with the duplication/random loss model, but more mitochondrial genes move in a pattern inconsistent with this model. An increased rate of mitochondrial gene rearrangement is not tightly associated with the evolution of parasitism. Although parasitic lineages tend to have more mitochondrial gene rearrangements than nonparasitic lineages, there are exceptions (e.g., Orussus and Schlettererius). It is likely that only a small proportion of the total number of mitochondrial gene rearrangements that have occurred during the evolution of the Hymenoptera have been sampled in the present study.

  11. Biophysical insights into the intercalative interaction of surfactant cobalt(III) complexes of certain diimine ligands bound to yeast tRNA: Effects of hydrophobicity

    Science.gov (United States)

    Nagaraj, Karuppiah; Sakthinathan, Subramanian; Arunachalam, Sankaralingam

    2015-08-01

    The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)2(DA)2](ClO4)3 1 and cis-[Co(dpq)2(DA)2](ClO4)3 2 where ip = imidazo[4,5-f][1,10]phenanthroline and dpq = dipyrido[3,2-d:2‧-3‧-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.

  12. Biophysical insights into the intercalative interaction of surfactant cobalt(III) complexes of certain diimine ligands bound to yeast tRNA: Effects of hydrophobicity.

    Science.gov (United States)

    Nagaraj, Karuppiah; Sakthinathan, Subramanian; Arunachalam, Sankaralingam

    2015-08-01

    The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)₂(DA)₂](ClO₄)₃ 1 and cis-[Co(dpq)₂(DA)₂](ClO₄)₃ 2 where ip=imidazo[4,5-f][1,10]phenanthroline and dpq=dipyrido[3,2-d:2'-3'-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.

  13. Dose Limits for Man do not Adequately Protect the Ecosystem

    Energy Technology Data Exchange (ETDEWEB)

    Higley, Kathryn A.; Alexakhin, Rudolf M.; McDonald, Joseph C.

    2004-08-01

    It has been known for quite some time that different organisms display differing degrees of sensitivity to the effects of ionizing radiations. Some microorganisms such as the bacterium Micrococcus radiodurans, along with many species of invertebrates, are extremely radio-resistant. Humans might be categorized as being relatively sensitive to radiation, and are a bit more resistant than some pine trees. Therefore, it could be argued that maintaining the dose limits necessary to protect humans will also result in the protection of most other species of flora and fauna. This concept is usually referred to as the anthropocentric approach. In other words, if man is protected then the environment is also adequately protected. The ecocentric approach might be stated as; the health of humans is effectively protected only when the environment is not unduly exposed to radiation. The ICRP is working on new recommendations dealing with the protection of the environment, and this debate should help to highlight a number of relevant issues concerning that topic.

  14. Deferasirox pharmacokinetics in patients with adequate versus inadequate response

    Science.gov (United States)

    Chirnomas, Deborah; Smith, Amber Lynn; Braunstein, Jennifer; Finkelstein, Yaron; Pereira, Luis; Bergmann, Anke K.; Grant, Frederick D.; Paley, Carole; Shannon, Michael

    2009-01-01

    Tens of thousands of transfusion-dependent (eg, thalassemia) patients worldwide suffer from chronic iron overload and its potentially fatal complications. The oral iron chelator deferasirox has become commercially available in many countries since 2006. Although this alternative to parenteral deferoxamine has been a major advance for patients with transfusional hemosiderosis, a proportion of patients have suboptimal response to the maximum approved doses (30 mg/kg per day), and do not achieve negative iron balance. We performed a prospective study of oral deferasirox pharmacokinetics (PK), comparing 10 transfused patients with inadequate deferasirox response (rising ferritin trend or rising liver iron on deferasirox doses > 30 mg/kg per day) with control transfusion-dependent patients (n = 5) with adequate response. Subjects were admitted for 4 assessments: deferoxamine infusion and urinary iron measurement to assess readily chelatable iron; quantitative hepatobiliary scintigraphy to assess hepatic uptake and excretion of chelate; a 24-hour deferasirox PK study following a single 35-mg/kg dose of oral deferasirox; and pharmacogenomic analysis. Patients with inadequate response to deferasirox had significantly lower systemic drug exposure compared with control patients (P < .00001). Cmax, volume of distribution/bioavailability (Vd/F), and elimination half-life (t1/2) were not different between the groups, suggesting bioavailability as the likely discriminant. Effective dosing regimens for inadequately responding patients to deferasirox must be determined. This trial has been registered at http://www.clinicaltrials.gov under identifier NCT00749515. PMID:19724055

  15. Acute isoniazid toxicity and the need for adequate pyridoxine supplies.

    Science.gov (United States)

    Morrow, Lee E; Wear, Robert E; Schuller, Dan; Malesker, Mark

    2006-10-01

    A 25-year-old, 54-kg Hispanic man who had recently started multidrug therapy for pulmonary tuberculosis presented in status epilepticus after ingesting 9 g of isoniazid in a suicide attempt. Successful management of this patient required collaboration between several institutions to provide the large amount of necessary intravenous pyridoxine. Ultimately, this single overdose depleted the supply of intravenous pyridoxine for a significant region of the state of Nebraska. Isoniazid is commonly used to treat tuberculosis, but it is encountered relatively infrequently as the cause of an acute overdose. Severe isoniazid overdoses may present as seizure activity that is refractory to conventional antiepileptic therapy. Although intravenous pyridoxine is an effective antidote for isoniazid overdoses in patients presenting with status epilepticus, this agent has few indications and is typically stocked in limited quantities. In regions with large populations of patients who receive antituberculosis therapy, collaborative networks must be created to ensure that adequate supplies of intravenous pyridoxine (> or = 20 g) are available for effective treatment of isoniazid poisonings.

  16. Undergraduate UK nutrition education might not adequately address weight management.

    Science.gov (United States)

    Rogerson, David; Soltani, Hora; Copeland, Robert

    2016-02-01

    Weight management appears to be multidimensional and complex, and registered nutritionists might work to educate, promote and provide weight-management services to communities, groups and individuals. However, nutrition education might not adequately reflect the weight-management requirements of individuals and groups. The aim of the present study was to investigate if the Association for Nutrition's undergraduate core competency framework for accredited Nutrition degrees sufficiently reflects the weight-management needs and experiences of individuals. A qualitative investigation, conducted within critical realist ontology, was performed to understand the weight-management experiences of dieters and compare these with the Association for Nutrition's accreditation criteria for undergraduate Nutrition degrees. Framework analysis was used to identify and explain participants' experiences thematically and to compare these with the Association for Nutrition's core competency criteria. Participants (n 8) with weight-loss (n 4) and weight-maintenance experiences (n 4) were interviewed using semi-structured interviews to understand weight management at the agential level. Participants described knowledge, exercise, planning, psychological constructs and behaviour-change techniques, determinants of eating and social support as features of weight management. The competency criteria provided clear guidance on all aspects discussed by the group, apart from psychological constructs and behaviour-change techniques and social support. Accredited Nutrition courses might not fully reflect the weight-management needs and experiences of individuals. Nutritionists might require greater knowledge of psychology and behaviour change to better understand and accommodate their clients' weight-management needs.

  17. Determination of the Specificity Landscape for Ribonuclease P Processing of Precursor tRNA 5' Leader Sequences.

    Science.gov (United States)

    Niland, Courtney N; Zhao, Jing; Lin, Hsuan-Chun; Anderson, David R; Jankowsky, Eckhard; Harris, Michael E

    2016-08-19

    Maturation of tRNA depends on a single endonuclease, ribonuclease P (RNase P), to remove highly variable 5' leader sequences from precursor tRNA transcripts. Here, we use high-throughput enzymology to report multiple-turnover and single-turnover kinetics for Escherichia coli RNase P processing of all possible 5' leader sequences, including nucleotides contacting both the RNA and protein subunits of RNase P. The results reveal that the identity of N(-2) and N(-3) relative to the cleavage site at N(1) primarily control alternative substrate selection and act at the level of association not the cleavage step. As a consequence, the specificity for N(-1), which contacts the active site and contributes to catalysis, is suppressed. This study demonstrates high-throughput RNA enzymology as a means to globally determine RNA specificity landscapes and reveals the mechanism of substrate discrimination by a widespread and essential RNA-processing enzyme.

  18. Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli.

    Science.gov (United States)

    Knutsson Jenvert, Rose-Marie; Holmberg Schiavone, Lovisa

    2005-02-01

    Stringent factor is a ribosome-dependent ATP:GTP pyrophosphoryl transferase that synthesizes (p)ppGpp upon nutrient deprivation. It is activated by unacylated tRNA in the ribosomal amino-acyl site (A-site) but it is unclear how activation occurs. A His-tagged stringent factor was isolated by affinity-chromatography and precipitation. This procedure yielded a protein of high purity that displayed (a) a low endogenous pyrophosphoryl transferase activity that was inhibited by the antibiotic tetracycline; (b) a low ribosome-dependent activity that was inhibited by the A-site specific antibiotics thiostrepton, micrococcin, tetracycline and viomycin; (c) a tRNA- and ribosome-dependent activity amounting to 4500 pmol pppGpp per pmol stringent factor per minute. Footprinting analysis showed that stringent factor interacted with ribosomes that contained tRNAs bound in classical states. Maximal activity was seen when the ribosomal A-site was presaturated with unacylated tRNA. Less tRNA was required to reach maximal activity when stringent factor and unacylated tRNA were added simultaneously to ribosomes, suggesting that stringent factor formed a complex with tRNA in solution that had higher affinity for the ribosomal A-site. However, tRNA-saturation curves, performed at two different ribosome/stringent factor ratios and filter-binding assays, did not support this hypothesis.

  19. Monitoring the eye lens: which dose quantity is adequate?

    Energy Technology Data Exchange (ETDEWEB)

    Behrens, R [Physikalisch-Technische Bundesanstalt, Bundesallee 100, D-38116 Braunschweig (Germany); Dietze, G, E-mail: rolf.behrens@ptb.d [Paracelsusstrasse 7, D-38116 Braunschweig (Germany)

    2010-07-21

    Recent epidemiological studies suggest a rather low dose threshold (below 0.5 Gy) for the induction of a cataract of the eye lens. Some other studies even assume that there is no threshold at all. Therefore, protection measures have to be optimized and current dose limits for the eye lens may be reduced in the future. The question of which personal dose equivalent quantity is appropriate for monitoring the dose to the eye lens arises from this situation. While in many countries dosemeters calibrated in terms of the dose equivalent quantity H{sub p}(0.07) have been seen as being adequate for monitoring the dose to the eye lens, this might be questionable in the case of reduced dose limits and, thus, it may become necessary to use the dose equivalent quantity H{sub p}(3) for this purpose. To discuss this question, the dose conversion coefficients for the equivalent dose of the eye lens (in the following eye lens dose) were determined for realistic photon and beta radiation fields and compared with the values of the corresponding conversion coefficients for the different operational quantities. The values obtained lead to the following conclusions: in radiation fields where most of the dose comes from photons, especially x-rays, it is appropriate to use dosemeters calibrated in terms of H{sub p}(0.07) on a slab phantom, while in other radiation fields (dominated by beta radiation or unknown contributions of photon and beta radiation) dosemeters calibrated in terms of H{sub p}(3) on a slab phantom should be used. As an alternative, dosemeters calibrated in terms of H{sub p}(0.07) on a slab phantom could also be used; however, in radiation fields containing beta radiation with the end point energy near 1 MeV, an overestimation of the eye lens dose by up to a factor of 550 is possible.

  20. Improving access to adequate pain management in Taiwan.

    Science.gov (United States)

    Scholten, Willem

    2015-06-01

    There is a global crisis in access to pain management in the world. WHO estimates that 4.65 billion people live in countries where medical opioid consumption is near to zero. For 2010, WHO considered a per capita consumption of 216.7 mg morphine equivalents adequate, while Taiwan had a per capita consumption of 0.05 mg morphine equivalents in 2007. In Asia, the use of opioids is sensitive because of the Opium Wars in the 19th century and for this reason, the focus of controlled substances policies has been on the prevention of diversion and dependence. However, an optimal public health outcome requires that also the beneficial aspects of these substances are acknowledged. Therefore, WHO recommends a policy based on the Principle of Balance: ensuring access for medical and scientific purposes while preventing diversion, harmful use and dependence. Furthermore, international law requires that countries ensure access to opioid analgesics for medical and scientific purposes. There is evidence that opioid analgesics for chronic pain are not associated with a major risk for developing dependence. Barriers for access can be classified in the categories of overly restrictive laws and regulations; insufficient medical training on pain management and problems related to assessment of medical needs; attitudes like an excessive fear for dependence or diversion; and economic and logistical problems. The GOPI project found many examples of such barriers in Asia. Access to opioid medicines in Taiwan can be improved by analysing the national situation and drafting a plan. The WHO policy guidelines Ensuring Balance in National Policies on Controlled Substances can be helpful for achieving this purpose, as well as international guidelines for pain treatment.

  1. Enzymology of tRNA modification in the bacterial MnmEG pathway.

    Science.gov (United States)

    Armengod, M-Eugenia; Moukadiri, Ismaïl; Prado, Silvia; Ruiz-Partida, Rafael; Benítez-Páez, Alfonso; Villarroya, Magda; Lomas, Rodrigo; Garzón, María J; Martínez-Zamora, Ana; Meseguer, Salvador; Navarro-González, Carmen

    2012-07-01

    Among all RNAs, tRNA exhibits the largest number and the widest variety of post-transcriptional modifications. Modifications within the anticodon stem loop, mainly at the wobble position and purine-37, collectively contribute to stabilize the codon-anticodon pairing, maintain the translational reading frame, facilitate the engagement of the ribosomal decoding site and enable translocation of tRNA from the A-site to the P-site of the ribosome. Modifications at the wobble uridine (U34) of tRNAs reading two degenerate codons ending in purine are complex and result from the activity of two multi-enzyme pathways, the IscS-MnmA and MnmEG pathways, which independently work on positions 2 and 5 of the U34 pyrimidine ring, respectively, and from a third pathway, controlled by TrmL (YibK), that modifies the 2'-hydroxyl group of the ribose. MnmEG is the only common pathway to all the mentioned tRNAs, and involves the GTP- and FAD-dependent activity of the MnmEG complex and, in some cases, the activity of the bifunctional enzyme MnmC. The Escherichia coli MnmEG complex catalyzes the incorporation of an aminomethyl group into the C5 atom of U34 using methylene-tetrahydrofolate and glycine or ammonium as donors. The reaction requires GTP hydrolysis, probably to assemble the active site of the enzyme or to carry out substrate recognition. Inactivation of the evolutionarily conserved MnmEG pathway produces a pleiotropic phenotype in bacteria and mitochondrial dysfunction in human cell lines. While the IscS-MnmA pathway and the MnmA-mediated thiouridylation reaction are relatively well understood, we have limited information on the reactions mediated by the MnmEG, MnmC and TrmL enzymes and on the precise role of proteins MnmE and MnmG in the MnmEG complex activity. This review summarizes the present state of knowledge on these pathways and what we still need to know, with special emphasis on the MnmEG pathway.

  2. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma

    Directory of Open Access Journals (Sweden)

    Joanna Birch

    2016-10-01

    Full Text Available The cell's repertoire of transfer RNAs (tRNAs has been linked to cancer. Recently, the level of the initiator methionine tRNA (tRNAiMet in stromal fibroblasts has been shown to influence extracellular matrix (ECM secretion to drive tumour growth and angiogenesis. Here we show that increased tRNAiMet within cancer cells does not influence tumour growth, but drives cell migration and invasion via a mechanism that is independent from ECM synthesis and dependent on α5β1 integrin and levels of the translation initiation ternary complex. In vivo and ex vivo migration (but not proliferation of melanoblasts is significantly enhanced in transgenic mice which express additional copies of the tRNAiMet gene. We show that increased tRNAiMet in melanoma drives migratory, invasive behaviour and metastatic potential without affecting cell proliferation and primary tumour growth, and that expression of RNA polymerase III-associated genes (which drive tRNA expression are elevated in metastases by comparison with primary tumours. Thus, specific alterations to the cancer cell tRNA repertoire drive a migration/invasion programme that may lead to metastasis.

  3. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

    Directory of Open Access Journals (Sweden)

    Rongzhong Li

    2015-07-01

    Full Text Available While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.

  4. Direct regulation of tRNA and 5S rRNA gene transcription by Polo-like kinase 1.

    Science.gov (United States)

    Fairley, Jennifer A; Mitchell, Louise E; Berg, Tracy; Kenneth, Niall S; von Schubert, Conrad; Silljé, Herman H W; Medema, René H; Nigg, Erich A; White, Robert J

    2012-02-24

    Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase III (pol III) through direct binding and phosphorylation of transcription factor Brf1. During interphase, Plk1 promotes tRNA and 5S rRNA expression by phosphorylating Brf1 directly on serine 450. However, this stimulatory modification is overridden at mitosis, when elevated Plk1 activity causes Brf1 phosphorylation on threonine 270 (T270), which prevents pol III recruitment. Thus, although Plk1 enhances net tRNA and 5S rRNA production, consistent with its proliferation-stimulating function, it also suppresses untimely transcription when cells divide. Genomic instability is apparent in cells with Brf1 T270 mutated to alanine to resist Plk1-directed inactivation, suggesting that chromosome segregation is vulnerable to inappropriate pol III activity. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma

    Science.gov (United States)

    Birch, Joanna; Clarke, Cassie J.; Campbell, Andrew D.; Campbell, Kirsteen; Mitchell, Louise; Liko, Dritan; Kalna, Gabriela; Strathdee, Douglas; Sansom, Owen J.; Neilson, Matthew; Blyth, Karen

    2016-01-01

    ABSTRACT The cell's repertoire of transfer RNAs (tRNAs) has been linked to cancer. Recently, the level of the initiator methionine tRNA (tRNAiMet) in stromal fibroblasts has been shown to influence extracellular matrix (ECM) secretion to drive tumour growth and angiogenesis. Here we show that increased tRNAiMet within cancer cells does not influence tumour growth, but drives cell migration and invasion via a mechanism that is independent from ECM synthesis and dependent on α5β1 integrin and levels of the translation initiation ternary complex. In vivo and ex vivo migration (but not proliferation) of melanoblasts is significantly enhanced in transgenic mice which express additional copies of the tRNAiMet gene. We show that increased tRNAiMet in melanoma drives migratory, invasive behaviour and metastatic potential without affecting cell proliferation and primary tumour growth, and that expression of RNA polymerase III-associated genes (which drive tRNA expression) are elevated in metastases by comparison with primary tumours. Thus, specific alterations to the cancer cell tRNA repertoire drive a migration/invasion programme that may lead to metastasis. PMID:27543055

  6. The tRNA 30-end Processing Enzyme tRNase Z2 Contributes to Chloroplast Biogenesis in Rice

    Institute of Scientific and Technical Information of China (English)

    Tuan Long; Dong Guo; Dong He; Wenjie Shen; Xianghua Li

    2013-01-01

    tRNase Z (TRZ) is a ubiquitous endonuclease that removes the 30-trailer from precursor tRNAs during maturation. In yeast and animals, TRZ regulates the cell cycle via its (t)RNA processing activity;however, its physiological function in higher plants has not been well characterized. This study describes the identification of a rice (Oryza sativa) TRZ2 mutant; plants homozygous for the osatrz2 mutation were albinos with deficient chlorophyll content. A microscopic analysis of the mutant plants revealed that the transition of proplastids to chloroplasts was arrested at an early stage, and the number and size of the plastids in callus cells was substantially decreased. A genetic complementation test and an RNA interference analysis confirmed that disruption of OsaTRZ2 was responsible for the mutant phenotype. OsaTRZ2 is expressed in all rice tissues, but is preferentially expressed in leaves, sheathes, and calli. OsaTRZ2 was subcellularly localized in chloroplasts, and displayed tRNA 30-end processing activity in both in vitro and in vivo assays. In the osatrz2 mutants, transcription of plastid-encoded and nucleus-encoded RNA polymerases was severely reduced and moderately increased, respectively. These results suggest that the tRNA 30 processing activity of OsaTRZ2 contributes to chloroplast biogenesis.

  7. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Silke Leimkühler

    2017-01-01

    Full Text Available Modifications of transfer RNA (tRNA have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT. Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.

  8. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers.

    Science.gov (United States)

    Zhang, Jinwei; Ferré-DAmaré, Adrian R

    2016-04-01

    Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA) and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.

  9. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers

    Directory of Open Access Journals (Sweden)

    Jinwei Zhang

    2016-04-01

    Full Text Available Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.

  10. Several RNase T2 enzymes function in induced tRNA and rRNA turnover in the ciliate Tetrahymena

    DEFF Research Database (Denmark)

    Andersen, Kasper Langebjerg; Collins, Kathleen

    2012-01-01

    RNase T2 enzymes are produced by a wide range of organisms and have been implicated to function in diverse cellular processes, including stress-induced anticodon loop cleavage of mature tRNAs to generate tRNA halves. Here we describe a family of eight RNase T2 genes (RNT2A-RNT2H) in the ciliate...... Tetrahymena thermophila. We constructed strains lacking individual or combinations of these RNT2 genes that were viable but had distinct cellular and molecular phenotypes. In strains lacking only one Rnt2 protein or lacking a subfamily of three catalytically inactive Rnt2 proteins, starvation-induced tRNA...... fragments continued to accumulate, with only a minor change in fragment profile in one strain. We therefore generated strains lacking pairwise combinations of the top three candidates for Rnt2 tRNases. Each of these strains showed a distinct starvation-specific profile of tRNA and rRNA fragment accumulation...

  11. Relationships among the cyclostome braconid (Hymenoptera: Braconidae) subfamilies inferred from a mitochondrial tRNA gene rearrangement.

    Science.gov (United States)

    Dowton, M

    1999-03-01

    The arrangement of mitochondrial tRNA genes for lysine (K) and aspartate (D) from the junction of the cytochrome oxidase II and ATPase 8 genes was determined in a range of hymenopteran taxa. This indicated that the ancestral arrangement for the order is 'KD', as found in the Diptera (represented by Drosophila and Anopheles) and basal Orthoptera. Most Hymenoptera that evolved after the appearance of parasitism also have the 'KD' arrangement, including noncyclostome braconids. However, most cyclostome braconids have either a 'DK' or a 'DHK' arrangement (where 'H' refers to the tRNA gene for Histidine). In both cases, the aspartate tRNA gene is encoded on the mitochondrial N-strand, rather than the J-strand as is usually the case. This rearrangement identified a monophyletic group not previously recognized, consisting of Rogadinae + Braconinae + Gnamptodontinae + Histeromerinae + Rhyssalinae + Betylobraconinae + Opiinae + Alysiinae. Only one cyclostome subfamily (Doryctinae) retained the 'KD' arrangement, suggesting this to be the most basal of the cyclostome subfamilies, consistent with ectoparasitism being plesiomorphic for the cyclostomes. However, the Aphidiinae also retained the 'KD' arrangement, leaving unresolved the issue of whether they should be included within the cyclostomes.

  12. Factorisable Quasi-adequate Semigroups%因子拟适当半群

    Institute of Scientific and Technical Information of China (English)

    彭婷婷; 郭小江

    2011-01-01

    In this paper, we investigate a class of factorisable IC quasi-adequate semigroups,so-called, factorisable IC quasi-adequate semigroups of type-(H, I). Some characterizations of factorisable IC quasi-adequate semigroups of type-(H, I) are obtained. In particular, we prove that any IC quasi-adequate semigroup has a factorisable IC quasi-adequate subsemigroups of type-(H, I) and a band of cancellative monoids.

  13. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

    Science.gov (United States)

    Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

    2013-01-01

    Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

  14. The selective tRNA aminoacylation mechanism based on a single G•U pair.

    Science.gov (United States)

    Naganuma, Masahiro; Sekine, Shun-ichi; Chong, Yeeting Esther; Guo, Min; Yang, Xiang-Lei; Gamper, Howard; Hou, Ya-Ming; Schimmel, Paul; Yokoyama, Shigeyuki

    2014-06-26

    Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.

  15. Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases

    Science.gov (United States)

    Hou, Ya-Ming

    2016-01-01

    Summary Methyl transfer from S-adenosyl methionine (abbreviated as AdoMet) to biologically active molecules such as mRNAs and tRNAs is one of the most fundamental and widespread reactions in nature, occurring in all three domains of life. The measurement of kinetic constants of AdoMet-dependent methyl transfer is therefore important for understanding the reaction mechanism in the context of biology. When kinetic constants of methyl transfer are measured in steady state over multiple rounds of turnover, the meaning of these constants is difficult to define and is often limited by non-chemical steps of the reaction, such as product release after each turnover. Here the measurement of kinetic constants of methyl transfer by tRNA methyltransferases in rapid equilibrium binding condition for one methyl transfer is described. The advantage of such a measurement is that the meaning of kinetic constants can be directly assigned to the steps associated with the chemistry of methyl transfer, including the substrate binding affinity to the methyl transferase, the pre-chemistry re-arrangement of the active site, and the chemical step of methyl transfer. An additional advantage is that kinetic constants measured for one methyl transfer can be correlated with structural information of the methyl transferase to gain direct insight into its reaction mechanism. PMID:26965259

  16. Selective charging of tRNA isoacceptors induced by amino-acid starvation

    Science.gov (United States)

    Dittmar, Kimberly A; Sørensen, Michael A; Elf, Johan; Ehrenberg, Måns; Pan, Tao

    2005-01-01

    Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants of the translation rate of its codons. A recent theoretical model predicts that amino-acid starvation results in ‘selective charging' where the charging levels of some tRNA isoacceptors will be low and those of others will remain high. Here, we developed a microarray for the analysis of charged fractions of tRNAs and measured charging for all Escherichia coli tRNAs before and during leucine, threonine or arginine starvation. Before starvation, most tRNAs were fully charged. During starvation, the isoacceptors in the leucine, threonine or arginine families showed selective charging when cells were starved for their cognate amino acid, directly confirming the theoretical prediction. Codons read by isoacceptors that retain high charging can be used for efficient translation of genes that are essential during amino-acid starvation. Selective charging can explain anomalous patterns of codon usage in the genes for different families of proteins. PMID:15678157

  17. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria.

    Science.gov (United States)

    Thiaville, Patrick C; El Yacoubi, Basma; Köhrer, Caroline; Thiaville, Jennifer J; Deutsch, Chris; Iwata-Reuyl, Dirk; Bacusmo, Jo Marie; Armengaud, Jean; Bessho, Yoshitaka; Wetzel, Collin; Cao, Xiaoyu; Limbach, Patrick A; RajBhandary, Uttam L; de Crécy-Lagard, Valérie

    2015-12-01

    Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.

  18. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside.

    Science.gov (United States)

    Deutsch, Christopher; El Yacoubi, Basma; de Crécy-Lagard, Valérie; Iwata-Reuyl, Dirk

    2012-04-20

    The anticodon stem-loop (ASL) of transfer RNAs (tRNAs) drives decoding by interacting directly with the mRNA through codon/anticodon pairing. Chemically complex nucleoside modifications found in the ASL at positions 34 or 37 are known to be required for accurate decoding. Although over 100 distinct modifications have been structurally characterized in tRNAs, only a few are universally conserved, among them threonylcarbamoyl adenosine (t(6)A), found at position 37 in the anticodon loop of a subset of tRNA. Structural studies predict an important role for t(6)A in translational fidelity, and in vivo work supports this prediction. Although pioneering work in the 1970s identified the fundamental substrates for t(6)A biosynthesis, the enzymes responsible for its biosynthesis have remained an enigma. We report here the discovery that in bacteria four proteins (YgjD, YrdC, YjeE, and YeaZ) are both necessary and sufficient for t(6)A biosynthesis in vitro. Notably, YrdC and YgjD are members of universally conserved families that were ranked among the top 10 proteins of unknown function in need of functional characterization, while YeaZ and YjeE are specific to bacteria. This latter observation, coupled with the essentiality of all four proteins in bacteria, establishes this pathway as a compelling new target for antimicrobial development.

  19. The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition.

    Science.gov (United States)

    McShane, Ariel; Hok, Eveline; Tomberlin, Jensen; Eriani, Gilbert; Geslain, Renaud

    2016-01-01

    Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.

  20. Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria

    Science.gov (United States)

    Gott, Jonatha M.; Somerlot, Benjamin H.; Gray, Michael W.

    2010-01-01

    The mitochondrial genome of Physarum polycephalum encodes five tRNAs, four of which are edited by nucleotide insertion. Two of these tRNAs, tRNAmet1 and tRNAmet2, contain predicted mismatches at the beginning (proximal end) of the acceptor stem. In addition, the putative 5′ end of tRNAmet2 overlaps the 3′ end of a small, abundant, noncoding RNA, which we term ppoRNA. These anomalies led us to hypothesize that these two Physarum mitochondrial tRNAs undergo additional editing events. Here, we show that tRNAmet1 and tRNAmet2 each has a nonencoded G at its 5′ end. In contrast to the other nucleotides that are added to Physarum mitochondrial RNAs, these extra G residues are likely added post-transcriptionally based on (1) the absence of added G in precursor transcripts containing inserted C and AA residues, (2) the presence of potential intermediates characteristic of 5′ replacement editing, and (3) preferential incorporation of GTP into tRNA molecules under conditions that do not support transcription. This is the first report of both post-transcriptional nucleotide insertions and the addition of single Gs in P. polycephalum mitochondrial transcripts. We postulate that tRNAmet1 and tRNAmet2 are acted upon by an activity similar to that present in the mitochondria of certain other amoebozoons and chytrid fungi, suggesting that enzymes that repair the 5′ end of tRNAs may be widespread. PMID:20106952

  1. Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data

    Directory of Open Access Journals (Sweden)

    Persi Erez

    2012-02-01

    Full Text Available Abstract Background Taxa counting is a major problem faced by analysis of metagenomic data. The most popular method relies on analysis of 16S rRNA sequences, but some studies employ also protein based analyses. It would be advantageous to have a method that is applicable directly to short sequences, of the kind extracted from samples in modern metagenomic research. This is achieved by the technique proposed here. Results We employ specific peptides, deduced from aminoacyl tRNA synthetases, as markers for the occurrence of single genes in data. Sequences carrying these markers are aligned and compared with each other to provide a lower limit for taxa counts in metagenomic data. The method is compared with 16S rRNA searches on a set of known genomes. The taxa counting problem is analyzed mathematically and a heuristic algorithm is proposed. When applied to genomic contigs of a recent human gut microbiome study, the taxa counting method provides information on numbers of different species and strains. We then apply our method to short read data and demonstrate how it can be calibrated to cope with errors. Comparison to known databases leads to estimates of the percentage of novelties, and the type of phyla involved. Conclusions A major advantage of our method is its simplicity: it relies on searching sequences for the occurrence of just 4000 specific peptides belonging to the S61 subgroup of aaRS enzymes. When compared to other methods, it provides additional insight into the taxonomic contents of metagenomic data. Furthermore, it can be directly applied to short read data, avoiding the need for genomic contig reconstruction, and taking into account short reads that are otherwise discarded as singletons. Hence it is very suitable for a fast analysis of next generation sequencing data.

  2. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations.

    Science.gov (United States)

    Czech, Andreas; Fedyunin, Ivan; Zhang, Gong; Ignatova, Zoya

    2010-10-01

    Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.

  3. Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA) and HIV-1 nef Genes in Escherichia coli.

    Science.gov (United States)

    Mualif, Siti Aisyah; Teow, Sin-Yeang; Omar, Tasyriq Che; Chew, Yik Wei; Yusoff, Narazah Mohd; Ali, Syed A

    2015-01-01

    Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW) rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef), HIV-1 p24 (ca), and HIV-1 vif in NiCo21(DE3) E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

  4. 5′ Processing of tRNA Precursors Can Be Modulated by the Human La Antigen Phosphoprotein†

    OpenAIRE

    Fan, Hao; Goodier, John L.; Chamberlain, Joel R.; Engelke, David R.; Richard J. Maraia

    1998-01-01

    Eukaryotic precursor (pre)-tRNAs are processed at both ends prior to maturation. Pre-tRNAs and other nascent transcripts synthesized by RNA polymerase III are bound at their 3′ ends at the sequence motif UUUOH [3′ oligo(U)] by the La antigen, a conserved phosphoprotein whose role in RNA processing has been associated previously with 3′-end maturation only. We show that in addition to its role in tRNA 3′-end maturation, human La protein can also modulate 5′ processing of pre-tRNAs. Both the La...

  5. The site of hydrolysis by rabbit reticulocyte peptidyl-tRNA hydrolase is the 3'-AMP terminus of susceptible tRNA substrates.

    Science.gov (United States)

    Gross, M; Crow, P; White, J

    1992-01-25

    The preceding paper (Gross, M., Starn, T.K., Rundquist, C., Crow, P., White, J., Olin, A., and Wagner, T. (1992) J. Biol. Chem. 267, 2073-2079) reported the purification and partial characterization of rabbit reticulocyte peptidyl-tRNA hydrolase. In this article we demonstrate that, unlike bacterial and yeast peptidyl-tRNA hydrolase which act by deacylation, the reticulocyte enzyme hydrolyzes N-acylaminoacyl-tRNA to N-acylaminoacyl-AMP. Reticulocyte lysate has a separate enzyme, that we have isolated and termed aminoacyl-AMP deacylase, which hydrolyzes N-acylaminoacyl-AMP and aminoacyl-AMP, recycling the amino acid and nucleotide components. The action of this enzyme is relatively specific for the N-acylaminoacyl-AMP generated by peptidyl-tRNA hydrolase, since it is much less active with N-acylaminoacyl-adenosine and inactive with N-acylaminoacyl-ACCAC, N-acylaminoacyl-tRNA, or aminoacyl-tRNA. The tRNA product of peptidyl-tRNA hydrolase action is tRNA missing only its 3'-AMP terminus (tRNA(c-c)), since reaminoacylation requires tRNA nucleotidyltransferase but not CTP. The 3' exonucleolytic action of reticulocyte peptidyl-tRNA hydrolase is specific to susceptible tRNA substrates, since it does not hydrolyze CACCA, CACCA-N-acylamino acid, polyuridylic acid, or the 3' polyadenylate tail of globin mRNA, and, since its ability to hydrolyze Escherichia coli f[3H]Met-tRNA(fMet) is not reduced by excess 5 S or 28 S ribosomal RNA and is reduced only slightly by excess tRNA(c-c). Reticulocyte peptidyl-tRNA hydrolase also hydrolyzes th 3'-AMP terminus of deacylated tRNA. This property may explain why the 3'-terminal AMP of tRNA undergoes turnover in reticulocytes and reticulocyte lysate, since we find that such turnover in gel-filtered reticulocyte lysate is increased under conditions where aminoacylation is reduced.

  6. Structure, Mechanism, and Specificity of a Eukaryal tRNA Restriction Enzyme Involved in Self-Nonself Discrimination

    Directory of Open Access Journals (Sweden)

    Anupam K. Chakravarty

    2014-04-01

    Full Text Available tRNA restriction by anticodon nucleases underlies cellular stress responses and self-nonself discrimination in a wide range of taxa. Anticodon breakage inhibits protein synthesis, which, in turn, results in growth arrest or cell death. The eukaryal ribotoxin PaT secreted by Pichia acaciae inhibits growth of Saccharomyces cerevisiae via cleavage of tRNAGln(UUG. We find that recombinant PaT incises a synthetic tRNAGln(UUG stem-loop RNA by transesterification at a single site 3′ of the wobble uridine, yielding 2′,3′-cyclic phosphate and 5′-OH ends. Incision is suppressed by replacement of the wobble nucleobase with adenine or guanine. The crystal structure of PaT reveals a distinctive fold and active site, essential components of which are demonstrated by mutagenesis. Pichia acaciae evades self-toxicity via a distinctive intracellular immunity protein, ImmPaT, which binds PaT and blocks nuclease activity. Our results highlight the evolutionary diversity of tRNA restriction and immunity systems.

  7. GidA, a tRNA modification enzyme, contributes to the growth and virulence of Streptococcus suis serotype 2

    Directory of Open Access Journals (Sweden)

    Ting eGao

    2016-04-01

    Full Text Available Glucose-inhibited division protein (GidA, is a tRNA modification enzyme functioning together with MnmE in the addition of a carboxymethylaminomethyl group to position 5 of the anticodon wobble uridine of tRNA. Here, we report a GidA homologue from a Chinese isolate SC-19 of the zoonotic Streptococcus suis serotype 2 (SS2. gidA disruption led to a defective growth, increased capsule thickness, and reduced hemolytic activity. Moreover, the gidA deletion mutant (ΔgidA displayed reduced mortality and bacterial loads in mice, reduced ability of adhesion to and invasion in epithelial cells, and increased sensitivity to phagocytosis. The iTRAQ analysis identified 372 differentially expressed (182 up- and 190 down-regulated proteins in ΔgidA and SC-19. Numerous DNA replication, cell division and virulence associated proteins were downregulated, whereas many capsule synthesis enzymes were upregulated by gidA disruption. This is consistent with the phenotypes of the mutant. Thus, GidA is a translational regulator that plays an important role in the growth, cell division, capsule biosynthesis, and virulence of SS2. Our findings provide new insight into the regulatory function of GidA in bacterial pathogens.

  8. Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome

    Science.gov (United States)

    Adio, Sarah; Senyushkina, Tamara; Peske, Frank; Fischer, Niels; Wintermeyer, Wolfgang; Rodnina, Marina V.

    2015-06-01

    The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement.

  9. Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids

    Science.gov (United States)

    José, Marco V.; Morgado, Eberto R.; Guimarães, Romeu Cardoso; Zamudio, Gabriel S.; de Farías, Sávio Torres; Bobadilla, Juan R.; Sosa, Daniela

    2014-01-01

    Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state. PMID:25370377

  10. Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.

    Science.gov (United States)

    Arragain, Simon; Bimai, Ornella; Legrand, Pierre; Caillat, Sylvain; Ravanat, Jean-Luc; Touati, Nadia; Binet, Laurent; Atta, Mohamed; Fontecave, Marc; Golinelli-Pimpaneau, Béatrice

    2017-07-11

    Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermophilic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that (i) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and (ii) the ATP binding site, localized thanks to a protein-bound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sulfide, thus acting as a sulfur carrier.

  11. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection.

    Science.gov (United States)

    Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D; Ren, Qian; Burke, Jordan E; Lee, Seonghoon; Butcher, Samuel E; Jan, Eric

    2015-11-24

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame.

  12. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2.

    Science.gov (United States)

    Uno, M; Ito, K; Nakamura, Y

    1996-01-01

    The termination of protein synthesis in bacteria requires codon-specific polypeptide release factors RF-1 (UAG/UAA specific) and RF-2 (UGA/UAA specific). We have proposed that release factors mimic tRNA and recognize the stop codon for polypeptide release (Nakamura et al (1996) Cell 87, 147-150). In contrast to the textbook view, genetic experiments have indicated that Escherichia coli RF-2 terminates translation very weakly at UAA while Salmonella RF-2 decodes this signal efficiently. Moreover, an excess of E coli RF-2 was toxic to cells while an excess of Salmonella RF-2 was not. These two RF-2 proteins are identical except for 16 out of 365 amino acids. Fragment swap experiments and site-directed mutagenesis revealed that a residue at position 246 is solely responsible for these two phenotypes. Upon substituting Ala (equivalent to Salmonella RF-2) for Thr-246 of E coli RF-2, the protein acquired increased release activity for UAA as well as for UGA. These results led us to conclude that E coli RF-2 activity is potentially weak and that the amino acid at position 246 plays a crucial role, not for codon discrimination, but for stop codon recognition or polypeptide release, presumably constituting an essential moiety of tRNA mimicry or interacting with peptidyltransferase centers of the ribosome.

  13. Functional consequences of T-stem mutations in E. coli tRNA Thr UGU in vitro and in vivo

    DEFF Research Database (Denmark)

    Saks, Margaret E; Sanderson, Lee E; Choi, Daniel S;

    2011-01-01

    unable to support growth of E. coli or are less effective than the wild-type sequence. Since the inviable T-stem sequences are often present in other E. coli tRNAs, it appears that T-stem sequences in each tRNA body have evolved to optimize function in a different way. Although mutations of tRNAThr can...... to mutations in three T-stem base pairs in a quantitatively identical manner. However, tRNAThr differs from other tRNAs by also using its rare A52–C62 pair as a negative specificity determinant. Using a plasmid-based tRNA gene replacement strategy, we show that many of the tRNAThrUGU T-stem changes are either......The binding affinities between Escherichia coli EF-Tu and 34 single and double base-pair changes in the T stem of E. coli tRNAThrUGU were compared with similar data obtained previously for several aa-tRNAs binding to Thermus thermophilus EF-Tu. With a single exception, the two proteins bound...

  14. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection

    Science.gov (United States)

    Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

    2012-01-01

    Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg2+ concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon–anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell. PMID:22190491

  15. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.

    Science.gov (United States)

    Zegers, Ingrid; Gigot, Daniel; van Vliet, Françoise; Tricot, Catherine; Aymerich, Stéphane; Bujnicki, Janusz M; Kosinski, Jan; Droogmans, Louis

    2006-01-01

    The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.

  16. Crystallization and preliminary crystallographic analysis of tRNA (m{sup 7}G46) methyltransferase from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun, E-mail: mkteng@ustc.edu.cn; Niu, Liwen, E-mail: mkteng@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China)

    2008-08-01

    tRNA (m{sup 7}G46) methyltransferase from E. coli was overexpressed, purified and crystallized. Diffraction data were collected to 2.04 Å resolution. Transfer RNA (tRNA) (m{sup 7}G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N{sup 7}-methylguanosine (m{sup 7}G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His{sub 6} tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2{sub 1}.

  17. In search of an adequate yet affordable tutor in online learning networks

    NARCIS (Netherlands)

    Sloep, Peter; Van Rosmalen, Peter; Kester, Liesbeth; Brouns, Francis; Koper, Rob

    2006-01-01

    Sloep, P., van Rosmalen, P., Kester, L., Brouns, F. M. R., & Koper, E. J. R. (2006). In search of an adequate yet affordable tutor in online learning networks. In search of an adequate yet affordable tutor in online learning networks. Presentation at the 6th IEEE International Conference on Advanced

  18. 42 CFR 413.24 - Adequate cost data and cost finding.

    Science.gov (United States)

    2010-10-01

    ... basis of reimbursable cost must provide adequate cost data. This must be based on their financial and.... Adequate data capable of being audited is consistent with good business concepts and effective and efficient management of any organization, whether it is operated for profit or on a nonprofit basis. It is a...

  19. 40 CFR 152.20 - Exemptions for pesticides adequately regulated by another Federal agency.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Exemptions for pesticides adequately... PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PESTICIDE REGISTRATION AND CLASSIFICATION PROCEDURES Exemptions § 152.20 Exemptions for pesticides adequately regulated by another Federal agency. The pesticides...

  20. The enforceability of the human right to adequate food : a comparative study

    NARCIS (Netherlands)

    Wernaart, B.F.W.

    2013-01-01

    While the right to adequate food is often discussed in the context of developing countries, especially in situations where access to adequate food is a problem on a larger scale, this book focusses on the right to food in two Western countries in which theoretically the circumstances allow this righ

  1. 9 CFR 2.33 - Attending veterinarian and adequate veterinary care.

    Science.gov (United States)

    2010-01-01

    ... adequate veterinary care. (a) Each research facility shall have an attending veterinarian who shall provide adequate veterinary care to its animals in compliance with this section: (1) Each research facility shall... veterinary care. 2.33 Section 2.33 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE...

  2. Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code.

    Science.gov (United States)

    Bernhardt, Harold S

    2016-02-24

    We have previously proposed that tRNA(Gly) was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNA(Gly) sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNA(Ser) has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNA(Ser) is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNA(Ser) and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio's recent criticism of our proposal that tRNA(Gly) was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers.

  3. Sulfur transfer and activation by ubiquitin-like modifier system Uba4•Urm1 link protein urmylation and tRNA thiolation in yeast

    Directory of Open Access Journals (Sweden)

    André Jüdes

    2016-10-01

    Full Text Available Urm1 is a unique dual-function member of the ubiquitin protein family and conserved from yeast to man. It acts both as a protein modifier in ubiquitin-like urmylation and as a sulfur donor for tRNA thiolation, which in concert with the Elongator pathway forms 5-methoxy-carbonyl-methyl-2-thio (mcm5s2 modified wobble uridines (U34 in anticodons. Using Saccharomyces cerevisiae as a model to study a relationship between these two functions, we examined whether cultivation temperature and sulfur supply previously implicated in the tRNA thiolation branch of the URM1 pathway also contribute to proper urmylation. Monitoring Urm1 conjugation, we found urmylation of the peroxiredoxin Ahp1 is suppressed either at elevated cultivation temperatures or under sulfur starvation. In line with this, mutants with sulfur transfer defects that are linked to enzymes (Tum1, Uba4 required for Urm1 activation by thiocarboxylation (Urm1-COSH were found to maintain drastically reduced levels of Ahp1 urmylation and mcm5s2U34 modification. Moreover, as revealed by site specific mutagenesis, the S-transfer rhodanese domain (RHD in the E1-like activator (Uba4 crucial for Urm1-COSH formation is critical but not essential for protein urmylation and tRNA thiolation. In sum, sulfur supply, transfer and activation chemically link protein urmylation and tRNA thiolation. These are features that distinguish the ubiquitin-like modifier system Uba4•Urm1 from canonical ubiquitin family members and will help elucidate whether, in addition to their mechanistic links, the protein and tRNA modification branches of the URM1 pathway may also relate in function to one another.

  4. Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA and HIV-1 nef Genes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Siti Aisyah Mualif

    Full Text Available Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef, HIV-1 p24 (ca, and HIV-1 vif in NiCo21(DE3 E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

  5. In vitro substrate specificities of 3'-5' polymerases correlate with biological outcomes of tRNA 5'-editing reactions.

    Science.gov (United States)

    Long, Yicheng; Jackman, Jane E

    2015-07-22

    Protozoan mitochondrial tRNAs (mt-tRNAs) are repaired by a process known as 5'-editing. Mt-tRNA sequencing revealed organism-specific patterns of editing G-U base pairs, wherein some species remove G-U base pairs during 5'-editing, while others retain G-U pairs in the edited tRNA. We tested whether 3'-5' polymerases that catalyze the repair step of 5'-editing exhibit organism-specific preferences that explain the treatment of G-U base pairs. Biochemical and kinetic approaches revealed that a 3'-5' polymerase from Acanthamoeba castellanii tolerates G-U wobble pairs in editing substrates much more readily than several other enzymes, consistent with its biological pattern of editing.

  6. Construction of a UGA suppressor tRNA by modification in vitro of yeast tRNACys.

    Science.gov (United States)

    Vacher, J; Grosjean, H; de Henau, S; Finelli, J; Buckingham, R H

    1984-01-02

    In this paper we describe the construction of a yeast tRNACys UGA suppressor. After specific hydrolysis of the parent molecule, the first base of the anticodon GCA was replaced by a uracil. The resulting molecule, harboring a UCA anticodon, was injected into Xenopus laevis oocytes in order to test its biological activities. The level of aminoacylation was similar to that of the parent molecule. Readthrough of the UGA termination codon in beta-globin mRNA, coinjected with the tRNA, indicated suppressor activity; however, tRNACys (anticodon UCA) was a much less efficient suppressor than others tested under the same conditions. We see no post-transcriptional modification of the uracil in the anticodon wobble position after injection into oocytes. This may be related to the low suppressor activity; however, it is also possible that other features of tRNACys structure may be unadapted to efficient UCA anticodon function.

  7. Interaction of Ru(Ⅱ) Complex with Yeast tRNA Studied by Isothermal Titration Calorimetry

    Institute of Scientific and Technical Information of China (English)

    徐宏; 刘敛洪; 刘志刚; 梁毅; 张鹏; 杜芬; 周兵瑞; 计亮年

    2005-01-01

    The interaction of metal complex with RNA has been studied by isothermal titration calorimetry (ITC) for the first time. ITC experiments show that complex [Ru(phen)2MPIP]2+ {phen= 1,10-phenanthroline, MP[P-2-(4-methylphenyl)imidazo[4,5-f]-1, 10-phenanthroline} interacts with yeast tRNA in terms of a model for a singleset of identical sites through intercalation, which is consistent with our previous observation obtained from spectroscopic methods, and this binding process was driven by a moderately favorable enthalpy decrease in combination with a moderately favorable entropy increase, suggesting that ITC is an effective method for deep studying the interactions of metal complexes with RNA.

  8. Crystallization and preliminary crystallographic analysis of tRNA (m7G46) methyltransferase from Escherichia coli

    Science.gov (United States)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun; Niu, Liwen

    2008-01-01

    Transfer RNA (tRNA) (m7G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N 7-­methylguanosine (m7G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His6 tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P21. PMID:18678947

  9. Crystallization and preliminary crystallographic analysis of tRNA (m(7)G46) methyltransferase from Escherichia coli.

    Science.gov (United States)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun; Niu, Liwen

    2008-08-01

    Transfer RNA (tRNA) (m(7)G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-L-methionine (SAM) as the methyl-group donor to catalyze the formation of N(7)-methylguanosine (m(7)G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His(6) tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2(1).

  10. Global translational impacts of the loss of the tRNA modification t6A in yeast

    Directory of Open Access Journals (Sweden)

    Patrick C. Thiaville

    2015-12-01

    Full Text Available The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t6A37 leads to severe growth defects in baker’s yeast, phenotypes similar to those caused by defects in mcm5s2U34 synthesis. Mutants in mcm5s2U34 can be suppressed by overexpression of tRNALysUUU, but we show t6A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t6A and mcm5s2U are not determinants for each other’s formation. Our results suggest that t6A deficiency, like mcm5s2U deficiency, leads to protein folding defects, and show that the absence of t6A led to stress sensitivities (heat, ethanol, salt and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t6A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs were increased in the mutants. The global consequences on translation caused by t6A absence were examined by ribosome profiling. Interestingly, the absence of t6A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t6A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I34:C3 pairs while increasing the elongation rate of rare tRNAs and G34:U3 pairs. This work reveals that the consequences of t6A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes.

  11. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo.

    Directory of Open Access Journals (Sweden)

    Keshab Rijal

    2016-08-01

    Full Text Available The ability of RNA polymerase (RNAP III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC; they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.

  12. Global translational impacts of the loss of the tRNA modification t6A in yeast

    Science.gov (United States)

    Thiaville, Patrick C.; Legendre, Rachel; Rojas-Benítez, Diego; Baudin-Baillieu, Agnès; Hatin, Isabelle; Chalancon, Guilhem; Glavic, Alvaro; Namy, Olivier; de Crécy-Lagard, Valérie

    2015-01-01

    The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t6A37 leads to severe growth defects in baker’s yeast, phenotypes similar to those caused by defects in mcm5s2U34 synthesis. Mutants in mcm5s2U34 can be suppressed by overexpression of tRNALysUUU, but we show t6A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t6A and mcm5s2U are not determinants for each other’s formation. Our results suggest that t6A deficiency, like mcm5s2U deficiency, leads to protein folding defects, and show that the absence of t6A led to stress sensitivities (heat, ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t6A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs) were increased in the mutants. The global consequences on translation caused by t6A absence were examined by ribosome profiling. Interestingly, the absence of t6A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t6A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I34:C3 pairs while increasing the elongation rate of rare tRNAs and G34:U3 pairs. This work reveals that the consequences of t6A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes. PMID:26798630

  13. Abundant Semigroups with Q-adequate Transversals and Some of Their Special Cases

    Institute of Scientific and Technical Information of China (English)

    Xiaojiang Guo; K.P. Shum

    2007-01-01

    Regular semigroups with multiplicative inverse transversals were first studied by Blyth and McFadden in 1982.In this paper, we extend the concept of inverse transversals to some kind of quasi-ideal adequate transversals of abundant semigroups.Some characterization theorems of abundant semigroups with different kinds of quasiideal adequate transversals are obtained. In particular, the structure theory of abundant semigroups having different kinds of quasi-ideal adequate transversals is established. Some results obtained by Blyth, McAlister and McFadden on inverse transversals in regular semigroups are hence extended to abundant semigroups.

  14. Auditory information processing during adequate propofol anesthesia monitored by electroencephalogram bispectral index

    NARCIS (Netherlands)

    C. Kerssens (Chantal); J. Klein (Jan); A. van der Woerd; B. Bonke (Benno)

    2001-01-01

    textabstractMemory for intraoperative events may arise from inadequate anesthesia when the hypnotic state is not continuously monitored. Electroencephalogram bispectral index (BIS) enables monitoring of the hypnotic state and titration of anesthesia to an adequate level

  15. Auditory information processing during adequate propofol anesthesia monitored by electroencephalogram bispectral index

    NARCIS (Netherlands)

    C. Kerssens (Chantal); J. Klein (Jan); A. van der Woerd; B. Bonke (Benno)

    2001-01-01

    textabstractMemory for intraoperative events may arise from inadequate anesthesia when the hypnotic state is not continuously monitored. Electroencephalogram bispectral index (BIS) enables monitoring of the hypnotic state and titration of anesthesia to an adequate level

  16. The C-terminal region of thermophilic tRNA (m7G46) methyltransferase (TrmB) stabilizes the dimer structure and enhances fidelity of methylation.

    Science.gov (United States)

    Tomikawa, Chie; Ochi, Anna; Hori, Hiroyuki

    2008-05-15

    Transfer RNA (m(7)G46) methyltransferase catalyzes methyl-transfer from S-adenosyl-L-methionine to N(7) atom of the semi-conserved G46 base in tRNA. Aquifex aeolicus is a hyper thermophilic eubacterium that grows at close to 95 degrees C. A. aeolicus tRNA (m(7)G46) methyltransferase [TrmB] has an elongated C-terminal region as compared with mesophilic counterparts. In this study, the authors focused on the functions of this C-terminal region. Analytic gel filtration chromatography and amino acid sequencing reveled that the start point (Glu202) of the C-terminal region is often cleaved by proteases during purification steps and the C-terminal region tightly binds to another subunit even in the presence of 6M urea. Because the C-terminal region contains abundant basic amino acid residues, the authors assumed that some of these residues might be involved in tRNA binding. To address this idea, the authors prepared eight alanine substitution mutant proteins. However, measurements of initial velocities of these mutant proteins suggested that the basic amino acid residues in the C-terminal region are not involved in tRNA binding. The authors investigated effects of the deletion of the C-terminal region. Deletion mutant protein of the C-terminal region (the core protein) was precipitated by incubation at 85 degrees C, while the wild type protein was soluble at that temperature, demonstrating that the C-terminal region contributes to the protein stability at high temperatures. The core protein had a methyl-transfer activity to yeast tRNA(Phe) transcript. Furthermore, the core protein slowly methylated tRNA transcripts, which did not contain G46 base. Moreover, the modified base was identified as m(7)G by two-dimensional thin layer chromatography. Thus, the deletion of the C-terminal region causes nonspecific methylation of N(7) atom of guanine base(s) in tRNA transcripts.

  17. Is protein-energy intake adequate during dialysis treatment in hemodialysis patients ?

    OpenAIRE

    Trudeke (G) I. Struijk-Wielinga; Najoua Zanaki; Maryam Hdoudou; Peter J.M. Weijs

    2012-01-01

    Protein-energy wasting (PEW) is a strong predictor of mortality in patients with chronic kidney disease. Although PEW is caused by non nutritional conditions, research indicates that nutritional support that targets adequate protein intake improves outcome. During dialysis therapy in-centre meals and snacks are provided. The question is whether these meals provide adequate protein and energy intake considering external (at home) consumed meals? Indirect calorimetry and physical activity Le...

  18. Adequate sleep among adolescents is positively associated with health status and health-related behaviors

    OpenAIRE

    Jeng Yi-Jong; Wang Edward K; Chen Mei-Yen

    2006-01-01

    Abstract Background Amount of sleep is an important indicator of health and well-being in children and adolescents. Adequate sleep (AS: adequate sleep is defined as 6–8 hours per night regularly) is a critical factor in adolescent health and health-related behaviors. The present study was based on a health promotion project previously conducted on adolescents in Tao-Yuan County, Taiwan. The aim was to examine the relationship between AS during schooldays and excessive body weight, frequency o...

  19. Individual and contextual determinants of adequate maternal health care services in Kenya.

    Science.gov (United States)

    Achia, Thomas N O; Mageto, Lillian E

    2015-01-01

    This study aimed to examine individual and community level factors associated with adequate use of maternal antenatal health services in Kenya. Individual and community level factors associated with adequate use of maternal health care (MHC) services were obtained from the 2008-09 Kenya Demographic and Health Survey data set. Multilevel partial-proportional odds logit models were fitted using STATA 13.0 to quantify the relations of the selected covariates to adequate MHC use, defined as a three-category ordinal variable. The sample consisted of 3,621 women who had at least one live birth in the five-year period preceding this survey. Only 18 percent of the women had adequate use of MHC services. Greater educational attainment by the woman or her partner, higher socioeconomic status, access to medical insurance coverage, and greater media exposure were the individual-level factors associated with adequate use of MHC services. Greater community ethnic diversity, higher community-level socioeconomic status, and greater community-level health facility deliveries were the contextual-level factors associated with adequate use of MHC. To improve the use of MHC services in Kenya, the government needs to design and implement programs that target underlying individual and community level factors, providing focused and sustained health education to promote the use of antenatal, delivery, and postnatal care.

  20. A platform for discovery and quantification of modified ribonucleosides in RNA: Application to stress-induced reprogramming of tRNA modifications

    Science.gov (United States)

    Cai, Weiling Maggie; Chionh, Yok Hian; Hia, Fabian; Gu, Chen; Kellner, Stefanie; McBee, Megan E.; Ng, Chee Sheng; Pang, Yan Ling Joy; Prestwich, Erin G.; Lim, Kok Seong; Babu, I. Ramesh; Begley, Thomas J.; Dedon, Peter C.

    2016-01-01

    Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. The chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: 1) RNA isolation, 2) RNA purification, 3) RNA hydrolysis to individual ribonucleosides, 4) chromatographic resolution of ribonucleosides, 5) identification of the full set of modified ribonucleosides, 6) mass spectrometric quantification of ribonucleosides, 6) interrogation of ribonucleoside datasets, and 7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications. PMID:26253965

  1. Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.

    Directory of Open Access Journals (Sweden)

    John W Yarham

    2014-06-01

    Full Text Available Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i6A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i6A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i6A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNASer(UCN mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i6A37 modification. These data demonstrate that deficiencies of i6A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.

  2. Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.

    Science.gov (United States)

    Yarham, John W; Lamichhane, Tek N; Pyle, Angela; Mattijssen, Sandy; Baruffini, Enrico; Bruni, Francesco; Donnini, Claudia; Vassilev, Alex; He, Langping; Blakely, Emma L; Griffin, Helen; Santibanez-Koref, Mauro; Bindoff, Laurence A; Ferrero, Ileana; Chinnery, Patrick F; McFarland, Robert; Maraia, Richard J; Taylor, Robert W

    2014-06-01

    Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i6A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i6A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i6A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNASer(UCN) mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i6A37 modification. These data demonstrate that deficiencies of i6A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.

  3. A Facile Three-Component One-Pot Synthesis of Structurally Constrained Tetrahydrofurans, Which Are t-RNA Synthetase Inhibitor Analogues

    Institute of Scientific and Technical Information of China (English)

    LU,Chong-Dao; CHEN,Zhi-Yong; HU,Wen-Hao; MI,Ai-Qiao

    2004-01-01

    @@ A one-pot procedure for the efficient synthesis of a small library of t-RNA inhibitor analogues was developed. Thus,Rh2(OAc)4 catalyzed three-component 1,3-dipolar cycloaddition reactions of carbonyl ylides derived from diazoindan-1,3-dione and aldehydes with other dipolarophiles in 1,1,2,2-tetrachloroethane at 80 ℃ gave ring fused tetrahydrofurans having three stereocenters in good yield.

  4. Secondary structure and feature of mitochondrial tRNA genes of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae

    Directory of Open Access Journals (Sweden)

    Kwang Bae Yoon

    2015-09-01

    Full Text Available The complete mitogenome (NC_021119 of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae was annotated and characterized in our recent publication (http://www.ncbi.nlm.nih.gov/nuccore/NC_021119. Here we provide additional information on methods in detail for obtaining the complete sequence of M. ussuriensis mitogenome. In addition, we describe characteristics of 22 tRNA genes and secondary structure and feature of 22 tRNAs of M. ussuriensis mitogenome.

  5. Identification and sequence analysis of metazoan tRNA 3'-end processing enzymes tRNase Zs.

    Directory of Open Access Journals (Sweden)

    Zhikang Wang

    Full Text Available tRNase Z is the endonuclease responsible for removing the 3'-trailer sequences from precursor tRNAs, a prerequisite for the addition of the CCA sequence. It occurs in the short (tRNase Z(S and long (tRNase Z(L forms. Here we report the identification and sequence analysis of candidate tRNase Zs from 81 metazoan species. We found that the vast majority of deuterostomes, lophotrochozoans and lower metazoans have one tRNase Z(S and one tRNase Z(L genes, whereas ecdysozoans possess only a single tRNase Z(L gene. Sequence analysis revealed that in metazoans, a single nuclear tRNase Z(L gene is likely to encode both the nuclear and mitochondrial forms of tRNA 3'-end processing enzyme through mechanisms that include alternative translation initiation from two in-frame start codons and alternative splicing. Sequence conservation analysis revealed a variant PxKxRN motif, PxPxRG, which is located in the N-terminal region of tRNase Z(Ss. We also identified a previously unappreciated motif, AxDx, present in the C-terminal region of both tRNase Z(Ss and tRNase Z(Ls. The AxDx motif consisting mainly of a very short loop is potentially close enough to form hydrogen bonds with the loop containing the PxKxRN or PxPxRG motif. Through complementation analysis, we demonstrated the likely functional importance of the AxDx motif. In conclusion, our analysis supports the notion that in metazoans a single tRNase Z(L has evolved to participate in both nuclear and mitochondrial tRNA 3'-end processing, whereas tRNase Z(S may have evolved new functions. Our analysis also unveils new evolutionarily conserved motifs in tRNase Zs, including the C-terminal AxDx motif, which may have functional significance.

  6. A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids.

    Science.gov (United States)

    Ieong, Ka-Weng; Pavlov, Michael Y; Kwiatkowski, Marek; Ehrenberg, Måns; Forster, Anthony C

    2014-05-01

    There is evidence that tRNA bodies have evolved to reduce differences between aminoacyl-tRNAs in their affinity to EF-Tu. Here, we study the kinetics of incorporation of L-amino acids (AAs) Phe, Ala allyl-glycine (aG), methyl-serine (mS), and biotinyl-lysine (bK) using a tRNA(Ala)-based body (tRNA(AlaB)) with a high affinity for EF-Tu. Results are compared with previous data on the kinetics of incorporation of the same AAs using a tRNA(PheB) body with a comparatively low affinity for EF-Tu. All incorporations exhibited fast and slow phases, reflecting the equilibrium fraction of AA-tRNA in active ternary complex with EF-Tu:GTP before the incorporation reaction. Increasing the concentration of EF-Tu increased the amplitude of the fast phase and left its rate unaltered. This allowed estimation of the affinity of each AA-tRNA to EF-Tu:GTP during translation, showing about a 10-fold higher EF-Tu affinity for AA-tRNAs formed from the tRNA(AlaB) body than from the tRNA(PheB) body. At ∼1 µM EF-Tu, tRNA(AlaB) conferred considerably faster incorporation kinetics than tRNA(PheB), especially in the case of the bulky bK. In contrast, the swap to the tRNA(AlaB) body did not increase the fast phase fraction of N-methyl-Phe incorporation, suggesting that the slow incorporation of N-methyl-Phe had a different cause than low EF-Tu:GTP affinity. The total time for AA-tRNA release from EF-Tu:GDP, accommodation, and peptidyl transfer on the ribosome was similar for the tRNA(AlaB) and tRNA(PheB) bodies. We conclude that a tRNA body with high EF-Tu affinity can greatly improve incorporation of unnatural AAs in a potentially generalizable manner.

  7. A model for mis-sense error in protein synthesis: mis-charged cognate tRNA versus mis-reading of codon

    CERN Document Server

    Dutta, Annwesha

    2015-01-01

    The sequence of amino acid monomers in the primary structure of protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. Transfer RNA (tRNA) molecules, each species of which is "charged" with a specific amino acid, enters the ribosome and participates in the reading of the codon by the ribosome. Both mis-reading of mRNA codon and prior mis-charging of a tRNA can lead to "mis-sense" error, i.e,. erroneous substitution of a correct amino acid monomer by an incorrect one during the synthesis of a protein. We develop a theoretical model of protein synthesis that allows for both types of contributions to the "mis-sense" error. We report exact analytical formulae for several quantities that characterize the interplay of mis-charging of tRNA and mis-reading of mRNA. The average rate of elongation of ...

  8. Non-Conserved Residues in Clostridium acetobutylicum tRNAAla Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch

    Directory of Open Access Journals (Sweden)

    Liang-Chun Liu

    2015-09-01

    Full Text Available The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions between the tRNA and the leader RNA have been demonstrated to be necessary, but not sufficient, for efficient antitermination. In this study, we used the Clostridium acetobutylicum alaS gene, which encodes alanyl-tRNA synthetase, to investigate the specificity of the tRNA response. We show that the homologous C. acetobutylicum tRNAAla directs antitermination of the C. acetobutylicum alaS gene in vitro, but the heterologous Bacillus subtilis tRNAAla (with the same anticodon and acceptor end does not. Base substitutions at positions that vary between these two tRNAs revealed synergistic and antagonistic effects. Variation occurs primarily at positions that are not conserved in tRNAAla species, which indicates that these non-conserved residues contribute to optimal antitermination of the homologous alaS gene. This study suggests that elements in tRNAAla may have coevolved with the homologous alaS T box leader RNA for efficient antitermination.

  9. Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes.

    Science.gov (United States)

    Acker, Joël; Ozanne, Christophe; Kachouri-Lafond, Rym; Gaillardin, Claude; Neuvéglise, Cécile; Marck, Christian

    2008-10-01

    In eukaryotes, genes transcribed by RNA polymerase III (Pol III) carry their own internal promoters and as such, are transcribed as individual units. Indeed, a very few cases of dicistronic Pol III genes are yet known. In contrast to other hemiascomycetes, 5S rRNA genes of Yarrowia lipolytica are not embedded into the tandemly repeated rDNA units, but appear scattered throughout the genome. We report here an unprecedented genomic organization: 48 over the 108 copies of the 5S rRNA genes are located 3' of tRNA genes. We show that these peculiar tRNA-5S rRNA dicistronic genes are expressed in vitro and in vivo as Pol III transcriptional fusions without the need of the 5S rRNA gene-specific factor TFIIIA, the deletion of which displays a viable phenotype. We also report the existence of a novel putative non-coding Pol III RNA of unknown function about 70 nucleotide-long (RUF70), the 13 genes of which are devoid of internal Pol III promoters and located 3' of the 13 copies of the tDNA-Trp (CCA). All genes embedded in the various dicistronic genes, fused 5S rRNA genes, RUF70 genes and their leader tRNA genes appear to be efficiently transcribed and their products correctly processed in vivo.

  10. Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation

    Directory of Open Access Journals (Sweden)

    Angela W. S. Fung

    2015-12-01

    Full Text Available Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates.

  11. The local dynamics of unfolded versus folded tRNA in comparison to synthetic polyelectrolytes and the role of electrostatic interactions

    Science.gov (United States)

    Roh, Joon Ho; Tyagi, Madhu; Briber, Robert M.; Woodson, Sarah A.; Sokolov, Alexei

    2012-02-01

    The local dynamics of RNA is strongly coupled to biological functions such as ligand recognition and catalysis. We have used quasielastic neutron scattering spectroscopy to follow the local motion of RNA and a synthetic polyelectrolyte as a function of Mg2+ concentration. We have observed that increasing Mg+2 concentration increases the picosecond to nanosecond dynamics of hydrated tRNA while stabilizing the tRNA folded structure. Analyses of the atomic mean-squared displacement, relaxation time, persistence length, and fraction of mobile atoms showed that unfolded tRNA is more rigid than in the folded state. This same behavior was observed for sulfonated polystyrene indicating that the increased dynamics in arises from charge screening of the polyelectrolyte rather than specific interactions. These results are opposite to what is observed for proteins for the relationship between the unfolded/folded states and the internal dynamics where the folded state is observed to be more rigid than the unfolded state. We conclude that the local dynamics for both bio- and synthetic polymers are strongly influenced by the electrostatic environment.

  12. Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism.

    Science.gov (United States)

    Shaheen, Ranad; Abdel-Salam, Ghada M H; Guy, Michael P; Alomar, Rana; Abdel-Hamid, Mohamed S; Afifi, Hanan H; Ismail, Samira I; Emam, Bayoumi A; Phizicky, Eric M; Alkuraya, Fowzan S

    2015-09-28

    Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity. Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m(7)G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m(7)G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m(7)G46 modification causes a growth deficiency phenotype in yeast. Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification.

  13. Hetero subunit interaction and RNA recognition of yeast tRNA (m7G46) methyltransferase synthesized in a wheat germ cell-free translation system.

    Science.gov (United States)

    Muneyoshi, Yuki; Matsumoto, Keisuke; Tomikawa, Chie; Toyooka, Takashi; Ochi, Anna; Masaoka, Takashi; Endo, Yaeta; Hori, Hiroyuki

    2007-01-01

    Yeast tRNA (m(7)G46) methyltransferase contains two protein subunits (Trm8 and Trm82). The enzyme catalyzes a methyl-transfer from S-adenosyl-L-methionine to the N(7) atom of guanine at position 46 in tRNA. We deviced synthesis of active Trm8-Trm82 heterodimer in a wheat germ cell-free translation system. When Trm8 or Trm82 mRNA were used for a synthesis, Trm8 or Trm82 protein could be synthesized. Upon mixing the synthesized Trm8 and Trm82 proteins, no active Trm8-Trm82 heterodimer was produced. Active Trm8-Trm82 heterodimer was only synthesized under conditions, in which both Trm8 and Trm82 mRNAs were co-translated. To address the RNA recognition mechanism of the Trm8-Trm82 complex, we investigated methyl acceptance activities of eight truncated yeast tRNA(Phe) transcripts. In this meeting, we demonstrate that yeast Trm8-Trm82 has stricter recognition requirements for the tRNA molecule as compared to the bacterial enzyme, TrmB.

  14. Minimal Adequate Model of Unemployment Duration in the Post-Crisis Czech Republic

    Directory of Open Access Journals (Sweden)

    Adam Čabla

    2016-03-01

    Full Text Available Unemployment is one of the leading economic problems in a developed world. The aim of this paper is to identify the differences in unemployment duration in different strata in the post-crisis Czech Republic via building a minimal adequate model, and to quantify the differences. Data from Labour Force Surveys are used and since they are interval censored in nature, proper metodology must be used. The minimal adequate model is built through the accelerated failure time modelling, maximum likelihood estimates and likelihood ratio tests. Variables at the beginning are sex, marital status, age, education, municipality size and number of persons in a household, containing altogether 29 model parameters. The minimal adequate model contains 5 parameters and differences are found between men and women, the youngest category and the rest and the university educated and the rest. The estimated expected values, variances, medians, modes and 90th percentiles are provided for all subgroups.

  15. Imitation of suprasegmental patterns by five-year-old children with adequate and inadequate articulation.

    Science.gov (United States)

    Shadden, B B; Asp, C W; Tonkovich, J D; Mason, D

    1980-08-01

    Ten five-year-old children with adequate articulation skills and 10 five-year-old children with inadequate articulation skills were administered the Templin-Darley Test of Articulation and the Test of Rhythm and Intonation Patterns (TRIP). Differences between the adequate and inadequate groups in terms of the mean percentage correct and the correlations between TRIP and Templin-Darley Test scores within groups were statistically nonsignificant. Item analysis revealed no differences between groups in the pattern of performance on the three subtests of the TRIP or on specific test items. The possible effects of therapy enrollment on suprasegmental test performance are discussed, and future research needs are suggested.

  16. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

    Directory of Open Access Journals (Sweden)

    Pengfei Fang

    2015-12-01

    Full Text Available Aminoacyl-tRNA synthetases (aaRSs are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.

  17. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

    Science.gov (United States)

    Gorochowski, Thomas E.; Ignatova, Zoya; Bovenberg, Roel A.L.; Roubos, Johannes A.

    2015-01-01

    Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. PMID:25765653

  18. CARACTERIZACIÓN DEL TALLO ACEPTOR DEL tRNA MEDIANTE DESCRIPTORES LOCALES BASADOS EN CARGAS PARCIALES

    Directory of Open Access Journals (Sweden)

    Ray Marín

    2009-04-01

    Full Text Available En este trabajo se caracteriza la distribución de carga del tallo aceptor del tRNA, considerando todas las posibles combinaciones de pares Watson-Crick. El estudio se realizó con 256 fragmentos moleculares de 10 nucleótidos que modelan los tres primeros pares del tallo aceptor, la base diferenciadora y el extremo CCA. Para caracterizar los nucleótidos se proponen dos descriptores locales basados en la distribución de carga de las base nitrogenada de cada nucleótido, los cuales se calculan a partir de las cargas parciales de Mulliken obtenidas de cálculos HF/6-31G. La caracterización y clasificación de los tallos según estos descriptores mostró como la base diferenciadora tiene un comportamiento particular respecto a los demás nucleótidos del tallo y una fuerte influencia sobre el extremo CCA. La clasificación de nueve variaciones del tallo aceptor del tRNAAla mostró una buena relación estructura-actividad que pone en evidencia la bondad de los descriptores propuestos para caracterizar de manera local la distribución de carga de estas biomoléculas. 

  19. Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates

    Science.gov (United States)

    Bar-Yaacov, Dan; Frumkin, Idan; Yashiro, Yuka; Schlesinger, Orr; Bieri, Philipp; Greber, Basil; Ban, Nenad; Zarivach, Raz; Alfonta, Lital; Pilpel, Yitzhak; Suzuki, Tsutomu; Mishmar, Dan

    2016-01-01

    The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates). However, this mtDNA base is a thymine in 10% of the vertebrates and a guanine in the 23S rRNA of 95% of bacteria, suggesting alternative evolutionary solutions. m1A, uridine, or guanine may stabilize the local structure of mitochondrial and bacterial ribosomes. Experimental assessment of genome-edited Escherichia coli showed that unmodified adenine caused impaired protein synthesis and growth. Our findings revealed a conserved mechanism of rRNA modification that has been selected instead of DNA mutations to enable proper mitochondrial ribosome function. PMID:27631568

  20. Structure-function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

    Energy Technology Data Exchange (ETDEWEB)

    Meineke, Birthe; Shuman, Stewart, E-mail: s-shuman@ski.mskcc.org

    2012-06-05

    Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure-activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.

  1. Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

    Directory of Open Access Journals (Sweden)

    Adaikkalam Vellaichamy

    Full Text Available Prostate cancer remains the most common malignancy among men in United States, and there is no remedy currently available for the advanced stage hormone-refractory cancer. This is partly due to the incomplete understanding of androgen-regulated proteins and their encoded functions. Whole-cell proteomes of androgen-starved and androgen-treated LNCaP cells were analyzed by semi-quantitative MudPIT ESI- ion trap MS/MS and quantitative iTRAQ MALDI- TOF MS/MS platforms, with identification of more than 1300 high-confidence proteins. An enrichment-based pathway mapping of the androgen-regulated proteomic data sets revealed a significant dysregulation of aminoacyl tRNA synthetases, indicating an increase in protein biosynthesis- a hallmark during prostate cancer progression. This observation is supported by immunoblot and transcript data from LNCaP cells, and prostate cancer tissue. Thus, data derived from multiple proteomics platforms and transcript data coupled with informatics analysis provides a deeper insight into the functional consequences of androgen action in prostate cancer.

  2. Covalent crosslinking of tRNA1Val to 16S RNA at the ribosomal P site: identification of crosslinked residues.

    Science.gov (United States)

    Prince, J B; Taylor, B H; Thurlow, D L; Ofengand, J; Zimmermann, R A

    1982-09-01

    N-Acetylvalyl-tRNA1Val (AcVal-tRNA1Val) was bound to the P site of uniformly 32P-labeled 70S ribosomes from Escherichia coli and crosslinked to 16S RNA in the 30S ribosomal subunit by irradiation with light of 300-400 nm. To identify the crosslinked nucleotide in 16S RNA. AcVal-tRNA1Val-16S [32P]RNA was digested completely with RNase T1 and the band containing the covalently attached oligonucleotides from tRNA and rRNA was isolated by polyacrylamide gel electrophoresis. The crosslinked oligonucleotide, and the 32P-labeled rRNA moiety released from it by photoreversal of the crosslink at 254 nm, were then analyzed by secondary hydrolysis with pancreatic RNase A and RNase U2. The oligonucleotide derived from 16S RNA was found to be the evolutionarily conserved sequence, U-A-C-A-C-A-C-C-G1401, and the nucleotide crosslinked to tRNA1Val, C1400. The identity of the covalently attached residue in the tRNA was established by using AcVal-tRNA1Val-16S RNA prepared from unlabeled ribosomes. This complex was digested to completion with RNase T1 and the resulting RNA fragments were labeled at the 3' end with [5'-32P]pCp. The crosslinked T1 oligonucleotide isolated from the mixture yielded one major end-labeled component upon photoreversal. Chemical sequence analysis demonstrated that this product was derived from the anticodon-containing pentadecanucleotide of tRNA1Val, C-A-C-C-U-C-C-C-U-cmo5U-A-C-m6A-A-G39(cmo5U, 5-carboxymethoxyuridine). A similar study of the crosslinked oligonucleotide revealed that the residue covalently bound to 16S was cmo5U34, the 5' or wobble base of the anticodon. The adduct is believed to result from formation of a cyclobutane dimer between cmo5U34 of tRNA1Val and C1400 of the 16S RNA.

  3. 9 CFR 2.40 - Attending veterinarian and adequate veterinary care (dealers and exhibitors).

    Science.gov (United States)

    2010-01-01

    ... veterinary care (dealers and exhibitors). 2.40 Section 2.40 Animals and Animal Products ANIMAL AND PLANT... veterinary care to its animals in compliance with this section. (1) Each dealer and exhibitor shall employ an... adequate veterinary care and to oversee the adequacy of other aspects of animal care and use. (b)...

  4. The Unequal Effect of Adequate Yearly Progress: Evidence from School Visits

    Science.gov (United States)

    Brown, Abigail B.; Clift, Jack W.

    2010-01-01

    The authors report insights, based on annual site visits to elementary and middle schools in three states from 2004 to 2006, into the incentive effect of the No Child Left Behind Act's requirement that increasing percentages of students make Adequate Yearly Progress (AYP) in every public school. They develop a framework, drawing on the physics…

  5. 21 CFR 514.117 - Adequate and well-controlled studies.

    Science.gov (United States)

    2010-04-01

    ... of the Center for Veterinary Medicine (the Director) may, on the Director's own initiative or on the... adequate and well-controlled studies of a new animal drug is to distinguish the effect of the new animal drug from other influences, such as spontaneous change in the course of the disease, normal...

  6. 76 FR 51041 - Hemoglobin Standards and Maintaining Adequate Iron Stores in Blood Donors; Public Workshop

    Science.gov (United States)

    2011-08-17

    ... HUMAN SERVICES Food and Drug Administration Hemoglobin Standards and Maintaining Adequate Iron Stores in... workshop. The Food and Drug Administration (FDA) is announcing a public workshop entitled: ``Hemoglobin... discuss blood donor hemoglobin and hematocrit qualification standards in the United States, its impact...

  7. Getting adequate information across to colorectal cancer screening subjects can be difficult.

    NARCIS (Netherlands)

    Rijn, AF van; Rossum, L.G.M. van; Deutekom, M.; Laheij, R.J.F.; Bossuyt, P.M.; Fockens, P.; Dekker, E. den; Jansen, J.B.M.J.

    2008-01-01

    OBJECTIVES: Participation in screening should be the outcome of an informed decision. We evaluated whether invitees in the first Dutch colorectal cancer (CRC) screening programme were adequately informed after having received a detailed information leaflet. METHODS: A total of 20,623 subjects aged

  8. Science Education as a Contributor to Adequate Yearly Progress and Accountability Programs

    Science.gov (United States)

    Judson, Eugene

    2010-01-01

    The No Child Left Behind (NCLB) Act requires states to measure the adequate yearly progress (AYP) of each public school and local educational agency (LEA) and to hold schools and LEAs accountable for failing to make AYP. Although it is required that science be assessed in at least three grades, the achievement results from science examinations are…

  9. In Search of an Adequate Yet Affordable Tutor in Online Learning Networks

    NARCIS (Netherlands)

    Sloep, Peter; Van Rosmalen, Peter; Kester, Liesbeth; Brouns, Francis; Koper, Rob

    2007-01-01

    Sloep, P. B., Van Rosmalen, P., Kester, L., Brouns, F., & Koper, R. (2006). In Search of an Adequate Yet Affordable Tutor in Online Learning Networks. In Kinshuk, R. Koper, P. Kommers, P. Kirschner, D. G. Sampson & W. Didderen (Eds.), Sixth International Conference on Advanced Learning Technologies

  10. Protecting the Home and Adequate Housing - Living in a Caravan or Trailer as a Human Right

    NARCIS (Netherlands)

    Donders, Y.

    2016-01-01

    Many Roma, gypsies and travellers live in caravans or trailers, sometimes in together trailer parks or camps. This article analyses how this specific lifestyle connected to their housing is protected under the various regimes and provisions of international human rights law. Home and adequate housin

  11. African Americans, Economically Disadvantaged, or Attendance Rate Effects on Adequate Yearly Progress

    Science.gov (United States)

    Wilson, Sheena

    2013-01-01

    The purpose of this quantitative, nonexperimental study was to determine if and to what extent a difference existed in the percentage of African American students, percentage of economically disadvantaged students, and students' attendance rate in elementary schools that made adequate yearly progress (AYP) and those that did not make AYP in one…

  12. Access to adequate water in post-apartheid South African provinces ...

    African Journals Online (AJOL)

    2010-10-02

    Oct 2, 2010 ... agement of water resources in South Africa. ... supply services and that 50% were without adequate sanitation. (DWAF ... President Mbeki promised that 'within the next 5 years all ... This research has responded to debates about water service .... under the first category 'Piped Households' or 'Basic Access'.

  13. Understanding the pelvic pain mechanism is key to find an adequate therapeutic approach.

    Science.gov (United States)

    Van Kerrebroeck, Philip

    2016-06-25

    Pain is a natural mechanism to actual or potential tissue damage and involves both a sensory and an emotional experience. In chronic pelvic pain, localisation of pain can be widespread and can cause considerable distress. A multidisciplinary approach is needed in order to fully understand the pelvic pain mechanism and to identify an adequate therapeutic approach.

  14. Do sex assault victims receive adequate care? If not, you risk fines, violations.

    Science.gov (United States)

    2002-06-01

    Failure to collect evidence, inadequate care, and delays resulted in a New York City hospital being fined for providing inadequate care to a rape victim. These problems are common in the emergency department. Avoid asking sexual assault victims the same questions repeatedly. Determine the patient's primary concern and address it immediately. Examine patients in a private area with adequate space.

  15. Determinants of prompt and adequate care among presumed malaria cases in a community in eastern Rwanda

    NARCIS (Netherlands)

    Ingabire, Chantal Marie; Kateera, Fredrick; Hakizimana, Emmanuel; Rulisa, Alexis; Muvunyi, Claude; Mens, Petra; Koenraadt, Sander; Mutesa, Leon; Vugt, Van Michele; Borne, Van Den Bart; Alaii, Jane

    2016-01-01

    Background: In order to understand factors influencing fever/malaria management practices among community-based individuals, the study evaluated psychosocial, socio-demographic and environmental determinants of prompt and adequate healthcare-seeking behaviours. Methods: A quantitative household (

  16. Evaluating the Reliability of Selected School-Based Indices of Adequate Reading Progress

    Science.gov (United States)

    Wheeler, Courtney E.

    2010-01-01

    The present study examined the stability (i.e., 4-month and 12-month test-retest reliability) of six selected school-based indices of adequate reading progress. The total sampling frame included between 3970 and 5655 schools depending on the index and research question. Each school had at least 40 second-grade students that had complete Oral…

  17. The Relationship between Parental Involvement and Adequate Yearly Progress among Urban, Suburban, and Rural Schools

    Science.gov (United States)

    Ma, Xin; Shen, Jianping; Krenn, Huilan Y.

    2014-01-01

    Using national data from the 2007-08 School and Staffing Survey, we compared the relationships between parental involvement and school outcomes related to adequate yearly progress (AYP) in urban, suburban, and rural schools. Parent-initiated parental involvement demonstrated significantly positive relationships with both making AYP and staying off…

  18. Which Food Security Determinants Predict Adequate Vegetable Consumption among Rural Western Australian Children?

    Science.gov (United States)

    Godrich, Stephanie L; Lo, Johnny; Davies, Christina R; Darby, Jill; Devine, Amanda

    2017-01-03

    Improving the suboptimal vegetable consumption among the majority of Australian children is imperative in reducing chronic disease risk. The objective of this research was to determine whether there was a relationship between food security determinants (FSD) (i.e., food availability, access, and utilisation dimensions) and adequate vegetable consumption among children living in regional and remote Western Australia (WA). Caregiver-child dyads (n = 256) living in non-metropolitan/rural WA completed cross-sectional surveys that included questions on FSD, demographics and usual vegetable intake. A total of 187 dyads were included in analyses, which included descriptive and logistic regression analyses via IBM SPSS (version 23). A total of 13.4% of children in this sample had adequate vegetable intake. FSD that met inclusion criteria (p ≤ 0.20) for multivariable regression analyses included price; promotion; quality; location of food outlets; variety of vegetable types; financial resources; and transport to outlets. After adjustment for potential demographic confounders, the FSD that predicted adequate vegetable consumption were, variety of vegetable types consumed (p = 0.007), promotion (p = 0.017), location of food outlets (p = 0.027), and price (p = 0.043). Food retail outlets should ensure that adequate varieties of vegetable types (i.e., fresh, frozen, tinned) are available, vegetable messages should be promoted through food retail outlets and in community settings, towns should include a range of vegetable purchasing options, increase their reliance on a local food supply and increase transport options to enable affordable vegetable purchasing.

  19. How Much and What Kind? Identifying an Adequate Technology Infrastructure for Early Childhood Education. Policy Brief

    Science.gov (United States)

    Daugherty, Lindsay; Dossani, Rafiq; Johnson, Erin-Elizabeth; Wright, Cameron

    2014-01-01

    To realize the potential benefits of technology use in early childhood education (ECE), and to ensure that technology can help to address the digital divide, providers, families of young children, and young children themselves must have access to an adequate technology infrastructure. The goals for technology use in ECE that a technology…

  20. Perceptions of Teachers in Their First Year of School Restructuring: Failure to Make Adequate Yearly Progress

    Science.gov (United States)

    Moser, Sharon

    2010-01-01

    The 2007-2008 school year marked the first year Florida's Title I schools that did not made Adequate Yearly Progress (AYP) for five consecutive years entered into restructuring as mandated by the "No Child Left Behind Act" of 2001. My study examines the perceptions of teacher entering into their first year of school restructuring due to…

  1. Does the new conceptual framework provide adequate concepts for reporting relevant information about performance?

    NARCIS (Netherlands)

    Brouwer, A.; Faramarzi, A; Hoogendoorn, M.

    2014-01-01

    The basic question we raise in this paper is whether the 2013 Discussion Paper (DP 2013) on the Conceptual Framework provides adequate principles for reporting an entity’s performance and what improvements could be made in light of both user needs and evidence from academic literature. DP 2013 propo

  2. Maintaining adequate nutrient supply - Principles, decision-support tools, and best management practices [Chapter 6

    Science.gov (United States)

    Robert B. Harrison; Douglas A. Maguire; Deborah Page-Dumroese

    2011-01-01

    Maintaining adequate nutrient supply to maintain or enhance tree vigor and forest growth requires conservation of topsoil and soil organic matter. Sometimes nutrient amendments are also required to supplement inherent nutrient-pool limitations or replenish nutrients removed in harvested material. The goal is to maintain the productive potential of the soil and, when...

  3. Use of Linear Programming to Develop Cost-Efficient Minimized Nutritionally Adequate Health Promoting Food Baskets

    DEFF Research Database (Denmark)

    Parlesak, Alexandr; Tetens, Inge; Jensen, Jørgen Dejgård;

    2016-01-01

    using linear programming. The FBs were defined depending on the type of constraints applied: cultural acceptability (C), or dietary guidelines (D), or nutrient recommendations (N), or cultural acceptability and nutrient recommendations (CN), or dietary guidelines and nutrient recommendations (DN......: Use of linear programming facilitates the generation of low-cost food baskets that are nutritionally adequate, health promoting, and culturally acceptable....

  4. 42 CFR 438.207 - Assurances of adequate capacity and services.

    Science.gov (United States)

    2010-10-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS MANAGED CARE Quality Assessment and Performance Improvement Access Standards § 438.207 Assurances of adequate capacity and services. (a) Basic rule. The State... that is sufficient in number, mix, and geographic distribution to meet the needs of the anticipated...

  5. Utp22p acts in concert with Utp8p to channel aminoacyl-tRNA from the nucleolus to the nuclear tRNA export receptor Los1p but not Msn5p.

    Science.gov (United States)

    Eswara, Manoja B K; Clayton, Ashley; Mangroo, Dev

    2012-12-01

    Utp8p is an essential nucleolar protein that channels aminoacyl-tRNAs from aminoacyl-tRNA synthetases in the nucleolus to the nuclear tRNA export receptors located in the nucleoplasm and nuclear pore complex in Saccharomyces cerevisiae. Utp8p is also part of the U3 snoRNA-associated protein complex involved in 18S rRNA biogenesis in the nucleolus. We report that Utp22p, which is another member of the U3 snoRNA-associated protein complex, is also an intranuclear component of the nuclear tRNA export machinery. Depletion of Utp22p results in nuclear retention of mature tRNAs derived from intron-containing and intronless precursors. Moreover, Utp22p copurifies with the nuclear tRNA export receptor Los1p, the aminoacyl-tRNA synthetase Tys1p and Utp8p, but not with the RanGTPase Gsp1p and the nuclear tRNA export receptor Msn5p. Utp22p interacts directly with Utp8p and Los1p in a tRNA-independent manner in vitro. Utp22p also interacts directly with Tys1p, but this binding is stimulated when Tys1p is bound to tRNA. However, Utp22p, unlike Utp8p, does not bind tRNA saturably. These data suggest that Utp22p recruits Utp8p to aminoacyl-tRNA synthetases in the nucleolus to collect aminoacyl-tRNA and then accompanies the Utp8p-tRNA complex to deliver the aminoacyl-tRNAs to Los1p but not Msn5p. It is possible that Nrap/Nol6, the mammalian orthologue of Utp22p, plays a role in channelling aminoacyl-tRNA to the nuclear tRNA export receptor exportin-t.

  6. Calculation of the Cost of an Adequate Education in Kentucky: A Professional Judgment Approach

    Directory of Open Access Journals (Sweden)

    Deborah A. Verstegen

    2004-02-01

    Full Text Available What is an adequate education and how much does it cost? In 1989, Kentucky’s State Supreme Court found the entire system of education unconstitutional-“all of its parts and parcels”. The Court called for all children to have access to an adequate education, one that is uniform and has as its goal the development of seven capacities, including: (i “sufficient oral and written communication skills to enable students to function in a complex and rapidly changing civilization . . . .and (vii sufficient levels of academic or vocational skills to enable public school students to compete favorably with their counterparts in surrounding states, in academics or in the job market”. Now, over a decade later, key questions remain regarding whether these objectives have been fulfilled. This research is designed to calculate the cost of an adequate education by aligning resources to State standards, laws and objectives, using a professional judgment approach. Seven focus groups were convened for this purpose and the scholarly literature was reviewed to provide multiple inputs into study findings. The study produced a per pupil base cost for each of three prototype school districts and an total statewide cost, with the funding gap between existing revenue and the revenue needed for current operations of $1.097 billion per year (2001-02. Additional key resource requirements needed to achieve an adequate education, identified by professional judgment panels, include: (1 extending the school year for students and teachers, (2 adding voluntary half-day preschool for three and four year olds, and (3 raising teacher salaries. This increases the funding gap to $1.23 billion and suggests that significant new funding is required over time if the Commonwealth of Kentucky is to provide an adequate and equitable education of high quality for all children and youth as directed by the State Supreme Court.

  7. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment

    Energy Technology Data Exchange (ETDEWEB)

    Ling, Jiqiang; Peterson, Kaitlyn M.; Simonovic, Ivana; Cho, Chris; Soll, Dieter; Simonovic, Miljan (Yale); (UIC)

    2014-03-12

    Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular ?? with a threonine (Thr) anticodon, MST1 also recognizes an unusual ??, which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employs distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for ?? recognition, whereas the anticodon sequence is essential for aminoacylation of ??. The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate ??, reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix {alpha}11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.

  8. Mutations in the mitochondrial tRNA Ser(AGY) gene are associated with deafness, retinal degeneration, myopathy and epilepsy.

    Science.gov (United States)

    Tuppen, Helen A L; Naess, Karin; Kennaway, Nancy G; Al-Dosary, Mazhor; Lesko, Nicole; Yarham, John W; Bruhn, Helene; Wibom, Rolf; Nennesmo, Inger; Weleber, Richard G; Blakely, Emma L; Taylor, Robert W; McFarland, Robert

    2012-08-01

    Although over 200 pathogenic mitochondrial DNA (mtDNA) mutations have been reported to date, determining the genetic aetiology of many cases of mitochondrial disease is still not straightforward. Here, we describe the investigations undertaken to uncover the underlying molecular defect(s) in two unrelated Caucasian patients with suspected mtDNA disease, who presented with similar symptoms of myopathy, deafness, neurodevelopmental delay, epilepsy, marked fatigue and, in one case, retinal degeneration. Histochemical and biochemical evidence of mitochondrial respiratory chain deficiency was observed in the patient muscle biopsies and both patients were discovered to harbour a novel heteroplasmic mitochondrial tRNA (mt-tRNA)(Ser(AGY)) (MTTS2) mutation (m.12264C>T and m.12261T>C, respectively). Clear segregation of the m.12261T>C mutation with the biochemical defect, as demonstrated by single-fibre radioactive RFLP, confirmed the pathogenicity of this novel variant in patient 2. However, unusually high levels of m.12264C>T mutation within both COX-positive (98.4 ± 1.5%) and COX-deficient (98.2 ± 2.1%) fibres in patient 1 necessitated further functional investigations to prove its pathogenicity. Northern blot analysis demonstrated the detrimental effect of the m.12264C>T mutation on mt-tRNA(Ser(AGY)) stability, ultimately resulting in decreased steady-state levels of fully assembled complexes I and IV, as shown by blue-native polyacrylamide gel electrophoresis. Our findings expand the spectrum of pathogenic mutations associated with the MTTS2 gene and highlight MTTS2 mutations as an important cause of retinal and syndromic auditory impairment.

  9. Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.

    Science.gov (United States)

    Tsunoda, Masaru; Kusakabe, Yoshio; Tanaka, Nobutada; Ohno, Satoshi; Nakamura, Masashi; Senda, Toshiya; Moriguchi, Tomohisa; Asai, Norio; Sekine, Mitsuo; Yokogawa, Takashi; Nishikawa, Kazuya; Nakamura, Kazuo T

    2007-01-01

    The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA(Tyr)(GPsiA). Structural information for TyrRS-tRNA(Tyr) complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs-tRNA(Tyr)s pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNA(Tyr) recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNA(Tyr) pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNA(Tyr). On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.

  10. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system.

    Science.gov (United States)

    Wan, Leo C K; Mao, Daniel Y L; Neculai, Dante; Strecker, Jonathan; Chiovitti, David; Kurinov, Igor; Poda, Gennadiy; Thevakumaran, Neroshan; Yuan, Fang; Szilard, Rachel K; Lissina, Elena; Nislow, Corey; Caudy, Amy A; Durocher, Daniel; Sicheri, Frank

    2013-07-01

    The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t(6)A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with the bacterial-specific proteins YeaZ and YjeE, whereas in archaeal and eukaryotic systems, Kae1 operates as part of a larger macromolecular assembly called KEOPS with Bud32, Cgi121, Gon7 and Pcc1 subunits. Qri7 orthologues function in the mitochondria and may represent the most primitive member of the Kae1/Qri7/YgjD protein family. In accordance with previous findings, we confirm that Qri7 complements Kae1 function and uncover that Qri7 complements the function of all KEOPS subunits in growth, t(6)A biosynthesis and, to a partial degree, telomere maintenance. These observations suggest that Kae1 provides a core essential function that other subunits within KEOPS have evolved to support. Consistent with this inference, Qri7 alone is sufficient for t(6)A biosynthesis with Sua5 in vitro. In addition, the 2.9 Å crystal structure of Qri7 reveals a simple homodimer arrangement that is supplanted by the heterodimerization of YgjD with YeaZ in bacteria and heterodimerization of Kae1 with Pcc1 in KEOPS. The partial complementation of telomere maintenance by Qri7 hints that KEOPS has evolved novel functions in higher organisms.

  11. Cardiac abnormalities in diabetic patients with mutation in the mitochondrial tRNA {sup Leu(UUR)}Gene

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, Hiroshi [Hyogo Medical Center for Adults, Akashi (Japan); Shiotani, Hideyuki

    1999-11-01

    An A-to-G transition at position 3243 of the mitochondrial DNA is known to be a pathogenic factor for mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), diabetes and cardiomyopathy. This mutation causes dysfunction of the central nervous system in MELAS. Because the heart, as well as the brain and nervous system, is highly dependent on the energy produced by mitochondrial oxidation, these tissues are more vulnerable to mitochondrial defects. Cardiac abnormalities were assessed in 10 diabetic patients associated with this mutation using echocardiography and {sup 123}I-metaiodobenzylguanidine (MIBG) scintigraphy, and compared with 19 diabetic patients without the mutation. Duration of diabetes, therapy, control of blood glucose and diabetic complications, such as diabetic retinopathy and nephropathy, were not different between the 2 groups. Diabetic patients with the mutation had a significantly thicker interventricular septum (16.8{+-}3.7 vs 11.0{+-}1.6 mm, p<0.001) than those without the mutation. Fractional shortening was lower in diabetic patients with the mutation than those without it (30.7{+-}7.0 vs 42.5{+-}6.6, p<0.001). MIBG uptake on the delayed MIBG image was significantly lower in diabetic patients with the mutation than in those without the mutation (mean value of the heart to mediastinum ratio: 1.6{+-}0.2 vs 2.0{+-}0.4, p>0.05). In conclusion, left ventricular hypertrophy with or without abnormal wall motion and severely reduced MIBG uptake may be characteristic in diabetic patients with a mutation in the mitochondrial tRNA {sup Leu(UUR)} gene. (author)

  12. A catalytic intermediate and several flavin redox states stabilized by folate-dependent tRNA methyltransferase from Bacillus subtilis.

    Science.gov (United States)

    Hamdane, Djemel; Guerineau, Vincent; Un, Sun; Golinelli-Pimpaneau, Beatrice

    2011-06-14

    The flavoprotein TrmFO catalyzes the C5 methylation of uridine 54 in the TΨC loop of tRNAs using 5,10-methylenetetrahydrofolate (CH(2)THF) as a methylene donor and FAD as a reducing agent. Here, we report biochemical and spectroscopic studies that unravel the remarkable capability of Bacillus subtilis TrmFO to stabilize, in the presence of oxygen, several flavin-reduced forms, including an FADH(•) radical, and a catalytic intermediate endowed with methylating activity. The FADH(•) radical was characterized by high-field electron paramagnetic resonance and electron nuclear double-resonance spectroscopies. Interestingly, the enzyme exhibited tRNA methylation activity in the absence of both an added carbon donor and an external reducing agent, indicating that a reaction intermediate, containing presumably CH(2)THF and FAD hydroquinone, is present in the freshly purified enzyme. Isolation by acid treatment, under anaerobic conditions, of noncovalently bound molecules, followed by mass spectrometry analysis, confirmed the presence in TrmFO of nonmodified FAD. Addition of formaldehyde to the purified enzyme protects the reduced flavins from decay by probably preventing degradation of CH(2)THF. The absence of air-stable reduced FAD species during anaerobic titration of oxidized TrmFO, performed in the absence or presence of added CH(2)THF, argues against their thermodynamic stabilization but rather implicates their kinetic trapping by the enzyme. Altogether, the unexpected isolation of a stable catalytic intermediate suggests that the flavin-binding pocket of TrmFO is a highly insulated environment, diverting the reduced FAD present in this intermediate from uncoupled reactions.

  13. Use of Linear Programming to Develop Cost-Efficient Minimized Nutritionally Adequate Health Promoting Food Baskets

    DEFF Research Database (Denmark)

    Parlesak, Alexandr; Tetens, Inge; Jensen, Jørgen Dejgård

    2016-01-01

    Background: Food-Based Dietary Guidelines (FBDGs) are developed to promote healthier eating patterns, but increasing food prices may make healthy eating less affordable. The aim of this study was to design a range of cost-minimized nutritionally adequate health-promoting food baskets (FBs......) that help prevent both micronutrient inadequacy and diet-related non-communicable diseases at lowest cost. Methods: Average prices for 312 foods were collected within the Greater Copenhagen area. The cost and nutrient content of five different cost-minimized FBs for a family of four were calculated per day......: Use of linear programming facilitates the generation of low-cost food baskets that are nutritionally adequate, health promoting, and culturally acceptable....

  14. Is casual exposure to summer sunlight effective at maintaining adequate vitamin D status?

    Science.gov (United States)

    Diffey, Brian L

    2010-08-01

    The advice that an adequate vitamin D status can be achieved by short, casual exposure to summer sunlight is ubiquitous. This review will examine the value of this advice. The results of experimental studies on changes in serum 25-hydroxyvitamin D [25(OH)D] concentrations following ultraviolet exposure are interpreted in the context of human exposure to sunlight. It is shown that current advice about modest sun exposure during the summer months does little in the way of boosting overall 25(OH)D levels, while sufficient sun exposure that could achieve a worthwhile benefit would compromise skin health. Failure to understand the nature of human exposure to sunlight has led to misguided advice concerning the sun exposure necessary for an adequate vitamin D status.

  15. The relationship between social capital, social support and the adequate use of prenatal care.

    Science.gov (United States)

    Leal, Maria do Carmo; Pereira, Ana Paula Esteves; Lamarca, Gabriela de Almeida; Vettore, Mario Vianna

    2011-01-01

    This study investigated the relationship between social capital and social support and the adequate use of prenatal care. A follow-up study involving 1,485 pregnant women was conducted in two cities in the Rio de Janeiro State, Brazil. Demographic and socioeconomic characteristics, social support and social capital data were collected during the first trimester of pregnancy. The post-partum period included information on levels of prenatal care utilization, social networks, parity, obstetric and gestational risk and prenatal care attendance. Hierarchized multinomial logistic regression was used in the statistical analysis. Prenatal care use above adequate levels was associated with high social capital at the city level (aggregated social capital), socioeconomic status and working during pregnancy. Lower non-aggregated contextual and compositional social capital, gestational risk and pattern of prenatal care were associated with inadequate prenatal care utilization. Contextual social capital and social support were found to be social determinants for the appropriate use of prenatal care.

  16. Ensuring smokers are adequately informed: reflections on consumer rights, manufacturer responsibilities, and policy implications

    Science.gov (United States)

    Chapman, S; Liberman, J

    2005-01-01

    The right to information is a fundamental consumer value. Following the advent of health warnings, the tobacco industry has repeatedly asserted that smokers are fully informed of the risks they take, while evidence demonstrates widespread superficial levels of awareness and understanding. There remains much that tobacco companies could do to fulfil their responsibilities to inform smokers. We explore issues involved in the meaning of "adequately informed" smoking and discuss some of the key policy and regulatory implications. We use the idea of a smoker licensing scheme—under which it would be illegal to sell to smokers who had not demonstrated an adequate level of awareness—as a device to explore some of these issues. We also explore some of the difficulties that addiction poses for the notion that smokers might ever voluntarily assume the risks of smoking. PMID:16046703

  17. The concept of adequate causation and Max Weber's comparative sociology of religion.

    Science.gov (United States)

    Buss, A

    1999-06-01

    Max Weber's The Protestant Ethic and the Spirit of Capitalism, studied in isolation, shows mainly an elective affinity or an adequacy on the level of meaning between the Protestant ethic and the 'spirit' of capitalism. Here it is suggested that Weber's subsequent essays on 'The Economic Ethics of World Religions' are the result of his opinion that adequacy on the level of meaning needs and can be verified by causal adequacy. After some introductory remarks, particularly on elective affinity, the paper tries to develop the concept of adequate causation and the related concept of objective possibility on the basis of the work of v. Kries on whom Weber heavily relied. In the second part, this concept is used to show how the study of the economic ethics of India, China, Rome and orthodox Russia can support the thesis that the 'spirit' of capitalism, although it may not have been caused by the Protestant ethic, was perhaps adequately caused by it.

  18. The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC).

    Science.gov (United States)

    Golovina, Anna Y; Sergiev, Petr V; Golovin, Andrey V; Serebryakova, Marina V; Demina, Irina; Govorun, Vadim M; Dontsova, Olga A

    2009-06-01

    Transfer RNA is highly modified. Nucleotide 37 of the anticodon loop is represented by various modified nucleotides. In Escherichia coli, the valine-specific tRNA (cmo(5)UAC) contains a unique modification, N(6)-methyladenosine, at position 37; however, the enzyme responsible for this modification is unknown. Here we demonstrate that the yfiC gene of E. coli encodes an enzyme responsible for the methylation of A37 in tRNA(1)(Val). Inactivation of yfiC gene abolishes m(6)A formation in tRNA(1)(Val), while expression of the yfiC gene from a plasmid restores the modification. Additionally, unmodified tRNA(1)(Val) can be methylated by recombinant YfiC protein in vitro. Although the methylation of m(6)A in tRNA(1)(Val) by YfiC has little influence on the cell growth under standard conditions, the yfiC gene confers a growth advantage under conditions of osmotic and oxidative stress.

  19. Determination of the number of copies of genes coding for 5s-rRNA and tRNA in the genomes of 43 species of wheat and Aegilops

    Energy Technology Data Exchange (ETDEWEB)

    Vakhitov, V.A.; Gimalov, F.R.; Nikonorov, Yu.M.

    1986-10-01

    The number of 5s-rRNA and tRNA genes has been studied in 43 species of wheat and Aegilops differing in ploidy level, genomic composition and origin. It has been demonstrated that the repeatability of the 5s-rRNA and tRNA genes increases in wheat with increasing ploidy level, but not in proportion to the genome size. In Aegilops, in distinction from wheat, the relative as well as absolute number of 5s-RNA genes increases with increasing ploidy level. The proportion of the sequences coding for tRNA in the dipoloid and polyploid Aegilops species is practically similar, while the number of tRNA genes increases almost 2-3 times with increasing ploidy level. Large variability has been recorded between the species with similar genomic composition and ploidy level in respect of the number of the 5s-rRNA and tRNA genes. It has been demonstrated that integration of the initial genomes of the amphidiploids is accompanied by elimination of a particular part of these genomes. It has been concluded that the mechanisms of establishment and evolution of genomes in the intra- and intergeneric allopolyploids are not identical.

  20. Charging Levels of Four tRNA Species in Escherichia coli Rel+ and REL- Strains during Amino Acid Starvation: A Simple Model for the Effect of ppGpp on Translational Accuracy

    DEFF Research Database (Denmark)

    Sørensen, M.A.

    2001-01-01

    tenfold to 40-fold. This reduction corresponds much better with the decreased rate of protein synthesis during starvation than that reported earlier. The determination of the charging levels of tRNA2Arg and tRNA1Thr during starvation were accurate enough to demonstrate that charging levels were at least......Escherichia coli strains mutated in the relA gene lack the ability to produce ppGpp during amino acid starvation. One consequence of this deficiency is a tenfold increase in misincorporation at starved codons compared to the wild-type. Previous work had shown that the charging levels of tRNAs were...... the same in Rel+ and Rel- strains and reduced, at most, two- to fivefold in both strains during starvation. The present reinvestigation of the charging levels of tRNA2Arg, tRNA1Thr, tRNA1Leu and tRNAHis during starvation of isogenic Rel+ and Rel- strains showed that starvation reduced charging levels...

  1. Which Food Security Determinants Predict Adequate Vegetable Consumption among Rural Western Australian Children?

    Directory of Open Access Journals (Sweden)

    Stephanie L. Godrich

    2017-01-01

    Full Text Available Improving the suboptimal vegetable consumption among the majority of Australian children is imperative in reducing chronic disease risk. The objective of this research was to determine whether there was a relationship between food security determinants (FSD (i.e., food availability, access, and utilisation dimensions and adequate vegetable consumption among children living in regional and remote Western Australia (WA. Caregiver-child dyads (n = 256 living in non-metropolitan/rural WA completed cross-sectional surveys that included questions on FSD, demographics and usual vegetable intake. A total of 187 dyads were included in analyses, which included descriptive and logistic regression analyses via IBM SPSS (version 23. A total of 13.4% of children in this sample had adequate vegetable intake. FSD that met inclusion criteria (p ≤ 0.20 for multivariable regression analyses included price; promotion; quality; location of food outlets; variety of vegetable types; financial resources; and transport to outlets. After adjustment for potential demographic confounders, the FSD that predicted adequate vegetable consumption were, variety of vegetable types consumed (p = 0.007, promotion (p = 0.017, location of food outlets (p = 0.027, and price (p = 0.043. Food retail outlets should ensure that adequate varieties of vegetable types (i.e., fresh, frozen, tinned are available, vegetable messages should be promoted through food retail outlets and in community settings, towns should include a range of vegetable purchasing options, increase their reliance on a local food supply and increase transport options to enable affordable vegetable purchasing.

  2. Adequate dosing of micronutrients for different age groups in the life cycle.

    Science.gov (United States)

    Bienz, Denise; Cori, Hector; Hornig, Dietrich

    2003-09-01

    Many studies of micronutrient supplementation in developing countries have used single-nutrient supplements with either vitamins or minerals. However, people in these countries often suffer from multiple, rather than single, micronutrient deficiencies. The objective of this paper is to discuss the factors that go into determining the adequate dosing of vitamins and/or minerals for people of different ages. To elaborate on the adequacy of micronutrient doses in supplements, a model described by the US FNB was used, which calculates the difference between the mean observed intake for an individual and the estimated average requirement for a life stage and gender group. This model allows estimating the degree of confidence that a certain nutrient intake (from supplements and diet) is adequate. The US/Canadian DRI values have been used as the basis for these calculations, from which it can be concluded that a daily supplement of one RDA of each micronutrient is adequate to cover the personal requirements of all individuals in each respective age and gender group of the population, provided that 20 to 40% of an RDA is supplied by the diet--likely a realistic value for developing countries. DRI values vary significantly between different age groups, reflecting changing needs over a life cycle. With the objective of a supplement to be adequate and safe, the design of a one-for-all supplement covering all age groups is not realistic. Such a supplement would either underscore or surpass the required intake of some of the age groups. Additionally the dosage of certain micronutrients might exceed the upper level of intake for lower age groups. Therefore, it is suggested that three different supplements following the one RDA concept for all micronutrients be developed for research use in developing countries for the following age groups; 1 to 3 years, 4 to 13 years, and females > 14 years (excluding during pregnancy).

  3. Effective dose of dexmedetomidine to induce adequate sedation in elderly patients under spinal anesthesia

    OpenAIRE

    2015-01-01

    Background During sedation with dexmedetomidine, a dose adjustment may be needed based on the invasiveness of the procedure, the patient's general condition, and their age. We aim here to determine the effective dose (ED) of dexmedetomidine to induce an adequate depth of sedation in elderly patients undergoing spinal anesthesia. Methods In this study, 47 patients aged 65 years or older, American Society of Anesthesiologists physical status I or II, undergoing spinal anesthesia were included. ...

  4. Evaluation of lymph node numbers for adequate staging of Stage II and III colon cancer

    Directory of Open Access Journals (Sweden)

    Bumpers Harvey L

    2011-05-01

    Full Text Available Abstract Background Although evaluation of at least 12 lymph nodes (LNs is recommended as the minimum number of nodes required for accurate staging of colon cancer patients, there is disagreement on what constitutes an adequate identification of such LNs. Methods To evaluate the minimum number of LNs for adequate staging of Stage II and III colon cancer, 490 patients were categorized into groups based on 1-6, 7-11, 12-19, and ≥ 20 LNs collected. Results For patients with Stage II or III disease, examination of 12 LNs was not significantly associated with recurrence or mortality. For Stage II (HR = 0.33; 95% CI, 0.12-0.91, but not for Stage III patients (HR = 1.59; 95% CI, 0.54-4.64, examination of ≥20 LNs was associated with a reduced risk of recurrence within 2 years. However, examination of ≥20 LNs had a 55% (Stage II, HR = 0.45; 95% CI, 0.23-0.87 and a 31% (Stage III, HR = 0.69; 95% CI, 0.38-1.26 decreased risk of mortality, respectively. For each six additional LNs examined from Stage III patients, there was a 19% increased probability of finding a positive LN (parameter estimate = 0.18510, p Conclusions Thus, the 12 LN cut-off point cannot be supported as requisite in determining adequate staging of colon cancer based on current data. However, a minimum of 6 LNs should be examined for adequate staging of Stage II and III colon cancer patients.

  5. Differentiating the barriers to adequate prenatal care in Missouri, 1987-88.

    OpenAIRE

    Sable, M R; Stockbauer, J W; Schramm, W F; Land, G H

    1990-01-01

    Inadequate prenatal care has previously been identified as a significant risk factor for women who have low birth weight infants and infants who die during the neonatal period. Postpartum interviews with 1,484 primarily low-income women were conducted during 1987-88 in three areas of Missouri with the highest rates of inadequate prenatal care. The purpose of the study was to identify barriers to prenatal care and to determine which barriers differentiated between women receiving adequate and ...

  6. Auditory information processing during adequate propofol anesthesia monitored by electroencephalogram bispectral index

    OpenAIRE

    Kerssens, Chantal; Klein, Jan; Woerd, A.; Bonke, Benno

    2001-01-01

    textabstractMemory for intraoperative events may arise from inadequate anesthesia when the hypnotic state is not continuously monitored. Electroencephalogram bispectral index (BIS) enables monitoring of the hypnotic state and titration of anesthesia to an adequate level (BIS 40 to 60). At this level, preserved memory function has been observed in trauma patients. We investigated memory formation in elective surgical outpatients during target-controlled propofol anesthesia supplemented with al...

  7. Current strategies for the restoration of adequate lordosis during lumbar fusion.

    Science.gov (United States)

    Barrey, Cédric; Darnis, Alice

    2015-01-18

    Not restoring the adequate lumbar lordosis during lumbar fusion surgery may result in mechanical low back pain, sagittal unbalance and adjacent segment degeneration. The objective of this work is to describe the current strategies and concepts for restoration of adequate lordosis during fusion surgery. Theoretical lordosis can be evaluated from the measurement of the pelvic incidence and from the analysis of spatial organization of the lumbar spine with 2/3 of the lordosis given by the L4-S1 segment and 85% by the L3-S1 segment. Technical aspects involve patient positioning on the operating table, release maneuvers, type of instrumentation used (rod, screw-rod connection, interbody cages), surgical sequence and the overall surgical strategy. Spinal osteotomies may be required in case of fixed kyphotic spine. AP combined surgery is particularly efficient in restoring lordosis at L5-S1 level and should be recommended. Finally, not one but several strategies may be used to achieve the need for restoration of adequate lordosis during fusion surgery.

  8. A one-item question with a Likert or Visual Analog Scale adequately measured current anxiety.

    Science.gov (United States)

    Davey, Heather M; Barratt, Alexandra L; Butow, Phyllis N; Deeks, Jonathan J

    2007-04-01

    To determine whether a single question with a Likert Scale or a Visual Analog Scale (VAS) response adequately measures current anxiety. Consecutive English-speaking adult women attending a dedicated breast clinic in a major Australian city were invited to complete a demographic questionnaire, the State Trait Anxiety Inventory (STAI), and a single question with a five-point Likert Scale response and a VAS in random order. Only women who completed the STAI were included in analyses. Four hundred of 497 (80%) eligible women agreed to participate. Both measures were adequate predictors of the STAI score; correlation with STAI was 0.78 (95% confidence interval [CI] 0.73-0.82) for the VAS and 0.75 (95% CI 0.70-0.79) for the Likert Scale. However, 11% of women incorrectly completed the VAS limiting its usefulness. A single question with either a Likert Scale or VAS response may be an adequate replacement for the STAI. Both measures quickly and easily assess anxiety and may be useful for research purposes when researchers have very limited time or questionnaire space or need to reduce the burden on participants of completing many measures.

  9. Current strategies for the restoration of adequate lordosis during lumbar fusion

    Science.gov (United States)

    Barrey, Cédric; Darnis, Alice

    2015-01-01

    Not restoring the adequate lumbar lordosis during lumbar fusion surgery may result in mechanical low back pain, sagittal unbalance and adjacent segment degeneration. The objective of this work is to describe the current strategies and concepts for restoration of adequate lordosis during fusion surgery. Theoretical lordosis can be evaluated from the measurement of the pelvic incidence and from the analysis of spatial organization of the lumbar spine with 2/3 of the lordosis given by the L4-S1 segment and 85% by the L3-S1 segment. Technical aspects involve patient positioning on the operating table, release maneuvers, type of instrumentation used (rod, screw-rod connection, interbody cages), surgical sequence and the overall surgical strategy. Spinal osteotomies may be required in case of fixed kyphotic spine. AP combined surgery is particularly efficient in restoring lordosis at L5-S1 level and should be recommended. Finally, not one but several strategies may be used to achieve the need for restoration of adequate lordosis during fusion surgery. PMID:25621216

  10. Global risk assessment of aflatoxins in maize and peanuts: are regulatory standards adequately protective?

    Science.gov (United States)

    Wu, Felicia; Stacy, Shaina L; Kensler, Thomas W

    2013-09-01

    The aflatoxins are a group of fungal metabolites that contaminate a variety of staple crops, including maize and peanuts, and cause an array of acute and chronic human health effects. Aflatoxin B1 in particular is a potent liver carcinogen, and hepatocellular carcinoma (HCC) risk is multiplicatively higher for individuals exposed to both aflatoxin and chronic infection with hepatitis B virus (HBV). In this work, we sought to answer the question: do current aflatoxin regulatory standards around the world adequately protect human health? Depending upon the level of protection desired, the answer to this question varies. Currently, most nations have a maximum tolerable level of total aflatoxins in maize and peanuts ranging from 4 to 20ng/g. If the level of protection desired is that aflatoxin exposures would not increase lifetime HCC risk by more than 1 in 100,000 cases in the population, then most current regulatory standards are not adequately protective even if enforced, especially in low-income countries where large amounts of maize and peanuts are consumed and HBV prevalence is high. At the protection level of 1 in 10,000 lifetime HCC cases in the population, however, almost all aflatoxin regulations worldwide are adequately protective, with the exception of several nations in Africa and Latin America.

  11. An adequate Fe nutritional status of maize suppresses infection and biotrophic growth of Colletotrichum graminicola.

    Science.gov (United States)

    Ye, Fanghua; Albarouki, Emad; Lingam, Brahmasivasenkar; Deising, Holger B; von Wirén, Nicolaus

    2014-07-01

    Iron (Fe) is an essential element for plant pathogens as well as for their host plants. As Fe plays a central role in pathogen virulence, most plants have evolved Fe-withholding strategies to reduce Fe availability to pathogens. On the other hand, plants need Fe for an oxidative burst in their basal defense response against pathogens. To investigate how the plant Fe nutritional status affects plant tolerance to a hemibiotrophic fungal pathogen, we employed the maize-Colletotrichum graminicola pathosystem. Fungal infection progressed rapidly via biotrophic to necrotrophic growth in Fe-deficient leaves, while an adequate Fe nutritional status suppressed the formation of infection structures of C. graminicola already during the early biotrophic growth phase. As indicated by Prussian blue and 3,3'-diaminobenzidine (DAB) staining, the retarding effect of an adequate Fe nutritional status on fungal development coincided temporally and spatially with the recruitment of Fe to infection sites and a local production of H2 O2 . A similar coincidence between local Fe and H2 O2 accumulation was found in a parallel approach employing C. graminicola mutants affected in Fe acquisition and differing in virulence. These results indicate that an adequate Fe nutritional status delays and partially suppresses the fungal infection process and the biotrophic growth phase of C. graminicola, most likely via the recruitment of free Fe to the fungal infection site for a timely oxidative burst. © 2014 Scandinavian Plant Physiology Society.

  12. A test for adequate wastewater treatment based on glutathione S transferase isoenzyme profile.

    Science.gov (United States)

    Grammou, A; Samaras, P; Papadimitriou, C; Papadopoulos, A I

    2013-04-01

    Discharge to the environment of treated or non-treated municipal wastewater imposes several threats to coastal and estuarine ecosystems which are difficult to assess. In our study we evaluate the use of the isoenzyme profile of glutathione S transferase (GST) in combination with the kinetic characteristics of the whole enzyme and of heme peroxidase, as a test of adequate treatment of municipal wastewater. For this reason, Artemia nauplii were incubated in artificial seawater prepared by wastewater samples, such as secondary municipal effluents produced by a conventional activated sludge unit and advanced treated effluents produced by the employment of coagulation, activated carbon adsorption and chlorination as single processes or as combined ones. Characteristic changes of the isoenzyme pattern and the enzymes' kinetic properties were caused by chlorinated secondary municipal effluent or by secondary non-chlorinated effluent. Advanced treatment by combination of coagulation and/or carbon adsorption resulted to less prominent changes, suggesting more adequate treatment. Our results suggest that GST isoenzyme profile in combination with the kinetic properties of the total enzyme family is a sensitive test for the evaluation of the adequateness of the treatment of reclaimed wastewater and the reduction of potentially harmful compounds. Potentially, it may offer a 'fingerprint' characteristic of a particular effluent and probably of the treatment level it has been subjected.

  13. Prevalence of the A1555G (12S rRNA and tRNA Ser(UCN mitochondrial mutations in hearing-impaired Brazilian patients

    Directory of Open Access Journals (Sweden)

    Abreu-Silva R.S.

    2006-01-01

    Full Text Available Mitochondrial mutations are responsible for at least 1% of the cases of hereditary deafness, but the contribution of each mutation has not yet been defined in African-derived or native American genetic backgrounds. A total of 203 unselected hearing-impaired patients were screened for the presence of the mitochondrial mutation A1555G in the 12S rRNA gene and mutations in the tRNA Ser(UCN gene in order to assess their frequency in the ethnically admixed Brazilian population. We found four individuals with A1555G mutation (2%, which is a frequency similar to those reported for European-derived populations in unselected samples. On the other hand, complete sequencing of the tRNA Ser(UCN did not reveal reported pathogenic substitutions, namely A7445G, 7472insC, T7510C, or T7511C. Instead, other rare substitutions were found such as T1291C, A7569G, and G7444A. To evaluate the significance of these findings, 110 "European-Brazilians" and 190 "African-Brazilians" unrelated hearing controls were screened. The T1291C, A7569G and G7444A substitutions were each found in about 1% (2/190 of individuals of African ancestry, suggesting that they are probably polymorphic. Our results indicate that screening for the A1555G mutation is recommended among all Brazilian deaf patients, while testing for mutations in the tRNA Ser(UCN gene should be considered only when other frequent deafness-causing mutations have been excluded or in the presence of a maternal transmission pattern.

  14. MD SIMULATION STUDIES TO INVESTIGATE ISO-ENERGETIC CONFORMATIONAL BEHAVIOUR OF MODIFIED NUCLEOSIDES M2G AND M22G PRESENT IN tRNA

    Directory of Open Access Journals (Sweden)

    Rohit S Bavi

    2013-02-01

    Full Text Available Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

  15. Prevalence of the A1555G (12S rRNA and tRNA Ser(UCN mitochondrial mutations in hearing-impaired Brazilian patients

    Directory of Open Access Journals (Sweden)

    R.S. Abreu-Silva

    2006-02-01

    Full Text Available Mitochondrial mutations are responsible for at least 1% of the cases of hereditary deafness, but the contribution of each mutation has not yet been defined in African-derived or native American genetic backgrounds. A total of 203 unselected hearing-impaired patients were screened for the presence of the mitochondrial mutation A1555G in the 12S rRNA gene and mutations in the tRNA Ser(UCN gene in order to assess their frequency in the ethnically admixed Brazilian population. We found four individuals with A1555G mutation (2%, which is a frequency similar to those reported for European-derived populations in unselected samples. On the other hand, complete sequencing of the tRNA Ser(UCN did not reveal reported pathogenic substitutions, namely A7445G, 7472insC, T7510C, or T7511C. Instead, other rare substitutions were found such as T1291C, A7569G, and G7444A. To evaluate the significance of these findings, 110 "European-Brazilians" and 190 "African-Brazilians" unrelated hearing controls were screened. The T1291C, A7569G and G7444A substitutions were each found in about 1% (2/190 of individuals of African ancestry, suggesting that they are probably polymorphic. Our results indicate that screening for the A1555G mutation is recommended among all Brazilian deaf patients, while testing for mutations in the tRNA Ser(UCN gene should be considered only when other frequent deafness-causing mutations have been excluded or in the presence of a maternal transmission pattern.

  16. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini: sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    Directory of Open Access Journals (Sweden)

    Daniela Silvestre

    2008-01-01

    Full Text Available At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini. The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced. We also report the genome organization (gene content and order, gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

  17. The transfer RNA genes in Oryza sativa L.ssp.indica

    Institute of Scientific and Technical Information of China (English)

    WANG; Xiyin(王希胤); SHI; Xiaoli(史晓黎); HAO; Bailin(郝柏林)

    2002-01-01

    The availability of the draft genome sequence of Oryza sativa L. ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.

  18. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold.

    Science.gov (United States)

    Ericsson, Ulrika B; Nordlund, Pär; Hallberg, B Martin

    2004-05-01

    Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

  19. Impact of P-Site tRNA and antibiotics on ribosome mediated protein folding: studies using the Escherichia coli ribosome.

    Directory of Open Access Journals (Sweden)

    Surojit Mondal

    Full Text Available BACKGROUND: The ribosome, which acts as a platform for mRNA encoded polypeptide synthesis, is also capable of assisting in folding of polypeptide chains. The peptidyl transferase center (PTC that catalyzes peptide bond formation resides in the domain V of the 23S rRNA of the bacterial ribosome. Proper positioning of the 3' -CCA ends of the A- and P-site tRNAs via specific interactions with the nucleotides of the PTC are crucial for peptidyl transferase activity. This RNA domain is also the center for ribosomal chaperoning activity. The unfolded polypeptide chains interact with the specific nucleotides of the PTC and are released in a folding competent form. In vitro transcribed RNA corresponding to this domain (bDV RNA also displays chaperoning activity. RESULTS: The present study explores the effects of tRNAs, antibiotics that are A- and P-site PTC substrate analogs (puromycin and blasticidin and macrolide antibiotics (erythromycin and josamycin on the chaperoning ability of the E. coli ribosome and bDV RNA. Our studies using mRNA programmed ribosomes show that a tRNA positioned at the P-site effectively inhibits the ribosome's chaperoning function. We also show that the antibiotic blasticidin (that mimics the interaction between 3'-CCA end of P/P-site tRNA with the PTC is more effective in inhibiting ribosome and bDV RNA chaperoning ability than either puromycin or the macrolide antibiotics. Mutational studies of the bDV RNA could identify the nucleotides U2585 and G2252 (both of which interact with P-site tRNA to be important for its chaperoning ability. CONCLUSION: Both protein synthesis and their proper folding are crucial for maintenance of a functional cellular proteome. The PTC of the ribosome is attributed with both these abilities. The silencing of the chaperoning ability of the ribosome in the presence of P-site bound tRNA might be a way to segregate these two important functions.

  20. Effect of chemical carcinogens and partial hepatectomy on in vivo ( sup 35 S)methionine interaction with rat liver tRNA

    Energy Technology Data Exchange (ETDEWEB)

    Kanduc, D.; Aresta, A.; Rossiello, M.R.; Ranieri, T.; Quagliariello, E. (Universita di Bari (Italy))

    1989-09-29

    The effect of carcinogens given by a single or multiple injections on the extent of ({sup 35}S)methionine interaction with hepatic tRNA was studied in normal and partially hepatectomized rats. Either partial hepatectomy or administration of ethionine (100 or 330 mg/kg body weight) and dimethylnitrosamine (120 mg/kg body weight) by multiple i.p. injections inhibited the ({sup 35}S)methionine-tRNA interaction, while administration of hepatocarcinogenic chemicals plus PH resulted rather in a stimulation. Methylnitrosourea enhanced the extent of interaction when administered in a single dose (100 mg per kg body weight) 18 h after partial hepatectomy.

  1. Adequate Iodine Status in New Zealand School Children Post-Fortification of Bread with Iodised Salt

    Science.gov (United States)

    Jones, Emma; McLean, Rachael; Davies, Briar; Hawkins, Rochelle; Meiklejohn, Eva; Ma, Zheng Feei; Skeaff, Sheila

    2016-01-01

    Iodine deficiency re-emerged in New Zealand in the 1990s, prompting the mandatory fortification of bread with iodised salt from 2009. This study aimed to determine the iodine status of New Zealand children when the fortification of bread was well established. A cross-sectional survey of children aged 8–10 years was conducted in the cities of Auckland and Christchurch, New Zealand, from March to May 2015. Children provided a spot urine sample for the determination of urinary iodine concentration (UIC), a fingerpick blood sample for Thyroglobulin (Tg) concentration, and completed a questionnaire ascertaining socio-demographic information that also included an iodine-specific food frequency questionnaire (FFQ). The FFQ was used to estimate iodine intake from all main food sources including bread and iodised salt. The median UIC for all children (n = 415) was 116 μg/L (females 106 μg/L, males 131 μg/L) indicative of adequate iodine status according to the World Health Organisation (WHO, i.e., median UIC of 100–199 μg/L). The median Tg concentration was 8.7 μg/L, which was <10 μg/L confirming adequate iodine status. There was a significant difference in UIC by sex (p = 0.001) and ethnicity (p = 0.006). The mean iodine intake from the food-only model was 65 μg/day. Bread contributed 51% of total iodine intake in the food-only model, providing a mean iodine intake of 35 μg/day. The mean iodine intake from the food-plus-iodised salt model was 101 μg/day. In conclusion, the results of this study confirm that the iodine status in New Zealand school children is now adequate. PMID:27196925

  2. Adequate Iodine Status in New Zealand School Children Post-Fortification of Bread with Iodised Salt

    Directory of Open Access Journals (Sweden)

    Emma Jones

    2016-05-01

    Full Text Available Iodine deficiency re-emerged in New Zealand in the 1990s, prompting the mandatory fortification of bread with iodised salt from 2009. This study aimed to determine the iodine status of New Zealand children when the fortification of bread was well established. A cross-sectional survey of children aged 8–10 years was conducted in the cities of Auckland and Christchurch, New Zealand, from March to May 2015. Children provided a spot urine sample for the determination of urinary iodine concentration (UIC, a fingerpick blood sample for Thyroglobulin (Tg concentration, and completed a questionnaire ascertaining socio-demographic information that also included an iodine-specific food frequency questionnaire (FFQ. The FFQ was used to estimate iodine intake from all main food sources including bread and iodised salt. The median UIC for all children (n = 415 was 116 μg/L (females 106 μg/L, males 131 μg/L indicative of adequate iodine status according to the World Health Organisation (WHO, i.e., median UIC of 100–199 μg/L. The median Tg concentration was 8.7 μg/L, which was <10 μg/L confirming adequate iodine status. There was a significant difference in UIC by sex (p = 0.001 and ethnicity (p = 0.006. The mean iodine intake from the food-only model was 65 μg/day. Bread contributed 51% of total iodine intake in the food-only model, providing a mean iodine intake of 35 μg/day. The mean iodine intake from the food-plus-iodised salt model was 101 μg/day. In conclusion, the results of this study confirm that the iodine status in New Zealand school children is now adequate.

  3. The Nigerian health care system: Need for integrating adequate medical intelligence and surveillance systems

    Directory of Open Access Journals (Sweden)

    Menizibeya Osain Welcome

    2011-01-01

    Full Text Available Objectives : As an important element of national security, public health not only functions to provide adequate and timely medical care but also track, monitor, and control disease outbreak. The Nigerian health care had suffered several infectious disease outbreaks year after year. Hence, there is need to tackle the problem. This study aims to review the state of the Nigerian health care system and to provide possible recommendations to the worsening state of health care in the country. To give up-to-date recommendations for the Nigerian health care system, this study also aims at reviewing the dynamics of health care in the United States, Britain, and Europe with regards to methods of medical intelligence/surveillance. Materials and Methods : Databases were searched for relevant literatures using the following keywords: Nigerian health care, Nigerian health care system, and Nigerian primary health care system. Additional keywords used in the search were as follows: United States (OR Europe health care dynamics, Medical Intelligence, Medical Intelligence systems, Public health surveillance systems, Nigerian medical intelligence, Nigerian surveillance systems, and Nigerian health information system. Literatures were searched in scientific databases Pubmed and African Journals OnLine. Internet searches were based on Google and Search Nigeria. Results : Medical intelligence and surveillance represent a very useful component in the health care system and control diseases outbreak, bioattack, etc. There is increasing role of automated-based medical intelligence and surveillance systems, in addition to the traditional manual pattern of document retrieval in advanced medical setting such as those in western and European countries. Conclusion : The Nigerian health care system is poorly developed. No adequate and functional surveillance systems are developed. To achieve success in health care in this modern era, a system well grounded in routine

  4. Are the current Australian sun exposure guidelines effective in maintaining adequate levels of 25-hydroxyvitamin D?

    Science.gov (United States)

    Kimlin, Michael; Sun, Jiandong; Sinclair, Craig; Heward, Sue; Hill, Jane; Dunstone, Kimberley; Brodie, Alison

    2016-01-01

    An adequate vitamin D status, as measured by serum 25-hydroxyvitamin D (25(OH)D) concentration, is important in humans for maintenance of healthy bones and muscle function. Serum 25(OH)D concentration was assessed in participants from Melbourne, Australia (37.81S, 144.96E), who were provided with the current Australian guidelines on sun exposure for 25(OH)D adequacy (25(OH)D ≥50 nmol/L). Participants were interviewed in February (summer, n=104) and August (winter, n=99) of 2013. Serum 25(OH)D concentration was examined as a function of measures of sun exposure and sun protection habits with control of key characteristics such as dietary intake of vitamin D, body mass index (BMI) and skin colour, that may modify this relationship. The mean 25(OH)D concentration in participants who complied with the current sun exposure guidelines was 67.3 nmol/L in summer and 41.9 nmol/L in winter. At the end of the study, 69.3% of participants who complied with the summer sun exposure guidelines were 25(OH)D adequate, while only 27.6% of participants who complied with the winter sun exposure guidelines were 25(OH)D adequate at the end of the study. The results suggest that the current Australian guidelines for sun exposure for 25(OH)D adequacy are effective for most in summer and ineffective for most in winter. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.

  5. Adequate X-ray control of central and peripheral vena cava catheters

    Energy Technology Data Exchange (ETDEWEB)

    Bostel, F.; Schmidt, C.

    1985-06-01

    Central venous catheters are frequently used not only in intensive care patients. Attention is drawn to the possible displacements of catheters and to the need for correct radiological control of the catheter position. Since unrecognized extravascular position of the catheter is followed by serious complications s.e. tension pneumothorax and infusions into the pleural cavity or the mediastinum, adequate X-ray control has to be carried out with simultaneous administration of contrast medium. Correction of displaced catheters should be done under fluoroscopy.

  6. A modified method for isolating mouse islets of an adequate quality, quantity, and purity.

    Science.gov (United States)

    Xu, Jiejie; Peng, Baogang; Zhang, Caiyun; Xu, Jiwei; Ma, Yi; Lu, Xinjun

    2017-08-01

    Mouse islets are widely used in diabetes research. Thus an adequate quality, quantity, and purity of islets are needed for high-quality investigations. We performed a combination of filtration and density gradient separation and optimized many steps in the islet isolation procedure, including perfusion, digestion, and purification. Our results show that an increased quality, quantity, and purity of isolated islets can be achieved using these modifications. Moreover, this method can guarantee maximal recovery and purity of the isolated islets and is easy to perform with practice.

  7. Enucleation for gastrointestinal stromal tumors at the esophagogastric junction: Is this an adequate solution?

    Institute of Scientific and Technical Information of China (English)

    Nadia Peparini; Giovanni Carbotta; Piero Chirletti

    2011-01-01

    The authors discussed the proposal by Coccolini and colleagues to treat gastrointestinal stromal tumors (GISTs) at the esophagogastric junction with enucleation and, if indicated, adjuvant therapy, reducing the risks related to esophageal and gastroesophageal resection. They concluded that, because the prognostic impact of a T1 high-mitotic rate on esophageal GIST is worse than that of a T1 high-mitotic rate on gastric GIST, enucleation may not be an adequate surgery for esophagogastric GISTs with a high mitotic rate in which the guarantee of negative resection margins and adjuvant therapies can be the only chance of survival.

  8. Towards {sup 31}Mg-β-NMR resonance linewidths adequate for applications in magnesium chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Stachura, M., E-mail: mstachura@triumf.ca [TRIUMF (Canada); McFadden, R. M. L. [University of British Columbia, Chemistry Department (Canada); Chatzichristos, A.; Dehn, M. H. [University of British Columbia, Department of Physics and Astronomy (Canada); Gottberg, A. [TRIUMF (Canada); Hemmingsen, L. [Københavns Universitet Universitetsparken 5, Kemisk Institut (Denmark); Jancso, A. [University of Szeged, Department of Inorganic and Analytical Chemistry (Hungary); Karner, V. L. [University of British Columbia, Chemistry Department (Canada); Kiefl, R. F. [University of British Columbia, Department of Physics and Astronomy (Canada); Larsen, F. H. [Københavns Universitet Rolighedsvej 26, Institut for Fødevarevidenskab (Denmark); Lassen, J.; Levy, C. D. P.; Li, R. [TRIUMF (Canada); MacFarlane, W. A. [University of British Columbia, Chemistry Department (Canada); Morris, G. D. [TRIUMF (Canada); Pallada, S. [CERN (Switzerland); Pearson, M. R. [TRIUMF (Canada); Szunyogh, D.; Thulstrup, P. W. [Københavns Universitet Universitetsparken 5, Kemisk Institut (Denmark); Voss, A. [University of Jyväskylä, Department of Physics (Finland)

    2017-11-15

    The span of most chemical shifts recorded in conventional {sup 25}Mg-NMR spectroscopy is ~ 100 ppm. Accordingly, linewidths of ~ 10 ppm or better are desirable to achieve adequate resolution for applications in chemistry. Here we present first high-field {sup 31}Mg- β-NMR measurements of {sup 31}Mg{sup +} ions implanted into a MgO single crystal carried out at the ISAC facility at TRIUMF. The resonances recorded at 2.5 T and 3.5 T show strong linewidth dependency on the applied RF power, ranging from ~ 419 ppm for the highest RF power down to ~ 48 ppm for the lowest one.

  9. Developing an adequate "pneumatraumatology": understanding the spiritual impacts of traumatic injury.

    Science.gov (United States)

    Bidwell, Duane R

    2002-01-01

    Psychosocial interventions and systematic theology are primary resources for chaplains and congregational pastors who care for victims of physical trauma. Yet these resources may not be adequate to address the spiritual impacts of trauma. This article proposes a preliminary "pneumatraumatology," drawing on early Christian asceticism and Buddhist mysticism to describe one way of understanding the spiritual impacts of traumatic injury. It also suggests possible responses to these impacts informed by narrative/constructionist perspectives and Breggemann's understanding of the dimensions of spiritual transformation in the Hebrew Bible.

  10. One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs

    2009-01-01

    Full Text Available Abstract Background The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1 ribozymic precursors of the synthetases seem to have used the same two sterically mirror modes of tRNA recognition, (2 having these two modes might have helped in preventing erroneous aminoacylation of ancestral tRNAs with complementary anticodons, yet (3 the risk of confusion for the presumably earliest pairs of complementarily encoded amino acids had little to do with anticodons. Accordingly, in this communication we focus on the acceptor stem. Results Our main result is the emergence of a palindrome structure for the acceptor stem's common ancestor, reconstructed from the phylogenetic trees of Bacteria, Archaea and Eukarya. In parallel, for pairs of ancestral tRNAs with complementary anticodons, we present updated evidence of concerted complementarity of the second bases in the acceptor stems. These two results suggest that the first pairs of "complementary" amino acids that were engaged in primordial coding, such as Gly and Ala, could have avoided erroneous aminoacylation if and only if the acceptor stems of their adaptors were recognized from the same, major groove, side. The class II protein synthetases then inherited this "primary preference" from isofunctional ribozymes. Conclusion Taken together, our results support the hypothesis that the genetic code per se (the one associated with the anticodons and the operational code of aminoacylation (associated with the acceptor diverged from a common ancestor that probably began developing before translation. The primordial advantage of linking some amino acids (most likely glycine and alanine to the ancestral acceptor stem may have been selective retention in a protocell surrounded by a leaky membrane for use in

  11. A Generalized Michaelis-Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon.

    Science.gov (United States)

    Dutta, Annwesha; Chowdhury, Debashish

    2017-05-01

    The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.

  12. Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes.

    Science.gov (United States)

    Mahapatra, Sahasransu; Dewari, Pooran S; Bhardwaj, Anubhav; Bhargava, Purnima

    2011-05-01

    FACT complex is involved in elongation and ensures fidelity in the initiation step of transcription by RNA polymerase (pol) II. Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes. We report here H2A.Z-chaperone activity of the yeast FACT complex on the short, nucleosome-free, non-coding, pol III-transcribed yeast tRNA genes. On a prototype gene, yeast SUP4, chromatin remodeler RSC and FACT regulate its transcription through novel mechanisms, wherein the two gene-flanking nucleosomes containing H2A.Z, play different roles. Nhp6, which ensures transcription fidelity and helps load yFACT onto the gene flanking nucleosomes, has inhibitory role. RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor. All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

  13. Congenital encephalomyopathy and adult-onset myopathy and diabetes mellitus: Different phenotypic associations of a new heteroplasmic mtDNA tRNA glutamic acid mutation

    Energy Technology Data Exchange (ETDEWEB)

    Hanna, M.G.; Nelson, I.; Sweeney, M.G.; Cooper, J.M.; Watkins, P.J.; Morgan-Hughes, J.A.; Harding, A.E. [Kings College Hospital, London (United Kingdom)

    1995-05-01

    We report the clinical, biochemical, and molecular genetic findings in a family with an unusual mitochondrial disease phenotype harboring a novel mtDNA tRNA glutamic acid mutation at position 14709. The proband and his sister presented with congenital myopathy and mental retardation and subsequently developed cerebellar ataxia. Other family members had either adult-onset diabetes mellitus with muscle weakness or adult-onset diabetes mellitus alone. Ragged-red and cytochrome c oxidase (COX)-negative fibers were present in muscle biopsies. Biochemical studies of muscle mitochondria showed reduced complex I and IV activities. The mtDNA mutation was heteroplasmic in blood and muscle in all matrilineal relatives analyzed. Primary myoblast, but not fibroblast, cultures containing high proportions of mutant mtDNA exhibited impaired mitochondrial translation. These observations indicate that mtDNA tRNA point mutations should be considered in the differential diagnosis of congenital myopathy. In addition they illustrate the diversity of phenotypes associated with this mutation in the same family and further highlight the association between mtDNA mutations and diabetes mellitus. 43 refs., 4 figs., 1 tab.

  14. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

    Directory of Open Access Journals (Sweden)

    John M Zaborske

    2014-12-01

    Full Text Available Natural selection favors efficient expression of encoded proteins, but the causes, mechanisms, and fitness consequences of evolved coding changes remain an area of aggressive inquiry. We report a large-scale reversal in the relative translational accuracy of codons across 12 fly species in the Drosophila/Sophophora genus. Because the reversal involves pairs of codons that are read by the same genomically encoded tRNAs, we hypothesize, and show by direct measurement, that a tRNA anticodon modification from guanosine to queuosine has coevolved with these genomic changes. Queuosine modification is present in most organisms but its function remains unclear. Modification levels vary across developmental stages in D. melanogaster, and, consistent with a causal effect, genes maximally expressed at each stage display selection for codons that are most accurate given stage-specific queuosine modification levels. In a kinetic model, the known increased affinity of queuosine-modified tRNA for ribosomes increases the accuracy of cognate codons while reducing the accuracy of near-cognate codons. Levels of queuosine modification in D. melanogaster reflect bioavailability of the precursor queuine, which eukaryotes scavenge from the tRNAs of bacteria and absorb in the gut. These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient.

  15. Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis.

    Science.gov (United States)

    Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C

    2014-05-01

    Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis.

  16. Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

    Science.gov (United States)

    Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

    2012-04-10

    Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. mTOR associates with TFIIIC, is found at tRNA and 5S rRNA genes, and targets their repressor Maf1.

    Science.gov (United States)

    Kantidakis, Theodoros; Ramsbottom, Ben A; Birch, Joanna L; Dowding, Sarah N; White, Robert J

    2010-06-29

    Synthesis of tRNA and 5S rRNA by RNA polymerase (pol) III is regulated by the mTOR pathway in mammalian cells. The mTOR kinase localizes to tRNA and 5S rRNA genes, providing an opportunity for direct control. Its presence at these sites can be explained by interaction with TFIIIC, a DNA-binding factor that recognizes the promoters of these genes. TFIIIC contains a TOR signaling motif that facilitates its association with mTOR. Maf1, a repressor that binds and inhibits pol III, is phosphorylated in a mTOR-dependent manner both in vitro and in vivo at serine 75, a site that contributes to its function as a transcriptional inhibitor. Proximity ligation assays confirm the interaction of mTOR with Maf1 and TFIIIC in nuclei. In contrast to Maf1 regulation in yeast, no evidence is found for nuclear export of Maf1 in response to mTOR signaling in HeLa cells. We conclude that mTOR associates with TFIIIC, is recruited to pol III-transcribed genes, and relieves their repression by Maf1.

  18. A kinetic framework for tRNA ligase and enforcement of a 2'-phosphate requirement for ligation highlights the design logic of an RNA repair machine.

    Science.gov (United States)

    Remus, Barbara S; Shuman, Stewart

    2013-05-01

    tRNA ligases are essential components of informational and stress-response pathways entailing repair of RNA breaks with 2',3'-cyclic phosphate and 5'-OH ends. Plant and fungal tRNA ligases comprise three catalytic domains. Phosphodiesterase and kinase modules heal the broken ends to generate the 3'-OH, 2'-PO₄, and 5'-PO₄ required for sealing by the ligase. We exploit RNA substrates with different termini to define rates of individual steps or subsets of steps along the repair pathway of plant ligase AtRNL. The results highlight rate-limiting transactions, how repair is affected by active-site mutations, and how mutations are bypassed by RNA alterations. We gain insights to 2'-PO₄ specificity by showing that AtRNL is deficient in transferring AMP to pRNAOH to form AppRNAOH but proficient at sealing pre-adenylylated AppRNAOH. This strategy for discriminating 2'-PO₄ versus 2'-OH ends provides a quality-control checkpoint to ensure that only purposeful RNA breaks are sealed and to avoid nonspecific "capping" of 5'-PO₄ ends.

  19. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.

    Science.gov (United States)

    Purta, Elzbieta; van Vliet, Françoise; Tricot, Catherine; De Bie, Lara G; Feder, Marcin; Skowronek, Krzysztof; Droogmans, Louis; Bujnicki, Janusz M

    2005-05-15

    The Escherichia coli TrmB protein and its Saccharomyces cerevisiae ortholog Trm8p catalyze the S-adenosyl-L-methionine-dependent formation of 7-methylguanosine at position 46 (m7G46) in tRNA. To learn more about the sequence-structure-function relationships of these enzymes we carried out a thorough bioinformatics analysis of the tRNA:m7G methyltransferase (MTase) family to predict sequence regions and individual amino acid residues that may be important for the interactions between the MTase and the tRNA substrate, in particular the target guanosine 46. We used site-directed mutagenesis to construct a series of alanine substitutions and tested the activity of the mutants to elucidate the catalytic and tRNA-recognition mechanism of TrmB. The functional analysis of the mutants, together with the homology model of the TrmB structure and the results of the phylogenetic analysis, revealed the crucial residues for the formation of the substrate-binding site and the catalytic center in tRNA:m7G MTases.

  20. Is Biomedical Waste Management Knowledge Adequate in Paramedics AND Sanitary Workers in Hospitals of Ujjain City?

    Directory of Open Access Journals (Sweden)

    Anand Rajput

    2016-03-01

    Full Text Available "Background: Hospitals produce a byproduct which is wasteful and causes contamination of the environment, with its antecedent complications. Inadequate and inappropriate knowledge of handling may have serious health consequences. Objectives: Present study was conducted to find out the current level of knowledge among paramedics (Lab Technicians, nursing staff and sanitary workers in hospitals of Ujjain city regarding biomedical waste management. Methods: A Cross-sectional study was conducted on 400 study participants in the Government and private hospital of Ujjain city from 1st January 2013 to 30 November 2013.Statistical analysis was done by SPSS 16.0 and chi-square test. Results: Mean age of the total 400 study participants was 31.36 (SD=11.62 years, among them 68.5% were female, majority (64.5% were the nurses and majority (64.7% were working in the concerned hospital since more than 2 years. Nursing staff has adequate knowledge (36.8% as compared to lab technician and sanitary staff (30.3%. Staff who had received medical waste management training had significantly (p<0.05 higher knowledge. Conclusion: On the basis of findings we conclude that the knowledge regarding biomedical waste management is not adequate among nursing staff, lab teqnicians and sanitary workers. " [Natl J Community Med 2016; 7(3.000: 151-154

  1. Incentives for an adequate, economic and reliable Swiss transmission grid. Final version

    Energy Technology Data Exchange (ETDEWEB)

    Twomey, P.; Neuhoff, K.; Newbery, D.

    2006-11-15

    This comprehensive final report for the Swiss Federal Office of Energy (SFOE) discusses incentives necessary for the implementation of an adequate, economic and reliable Swiss electricity transmission grid. As Switzerland moves towards a more liberalised and competitive electricity market, an essential task of policy makers will be to ensure that incentives are in place for the construction, maintenance and operation of adequate, economic and reliable transmission infrastructure. As well as continuing to serve the domestic market, the location of Switzerland at the centre of Europe also means that policy should embrace opportunities in servicing the developing European Internal Market by providing transit and other services. Topics discussed include the economic evaluation of transmission investment proposals, regulated transmission investment, investments in transmission lines by power merchants, power auctions and congestion management as well as inter-TSO compensation mechanisms. European regulations and practice are discussed as are access questions and transmission charges. Developments in interconnection management and harmonisation are examined. The particular characteristics of the Swiss energy system, its prices and its legal frameworks are discussed. Cross-border trading and security of supply are also discussed

  2. Maintaining Adequate CO2 Washout for an Advanced EMU via a New Rapid Cycle Amine Technology

    Science.gov (United States)

    Chullen, Cinda; Conger, Bruce

    2012-01-01

    Over the past several years, NASA has realized tremendous progress in Extravehicular Activity (EVA) technology development. This has been evidenced by the progressive development of a new Rapid Cycle Amine (RCA) system for the Advanced Extravehicular Mobility Unit (AEMU) Portable Life Support Subsystem (PLSS). The PLSS is responsible for the life support of the crew member in the spacesuit. The RCA technology is responsible for carbon dioxide (CO2) and humidity control. Another aspect of the RCA is that it is on-back vacuum-regenerable, efficient, and reliable. The RCA also simplifies the PLSS schematic by eliminating the need for a condensing heat exchanger for humidity control in the current EMU. As development progresses on the RCA, it is important that the sizing be optimized so that the demand on the PLSS battery is minimized. As well, maintaining the CO2 washout at adequate levels during an EVA is an absolute requirement of the RCA and associated ventilation system. Testing has been underway in-house at NASA Johnson Space Center and analysis has been initiated to evaluate whether the technology provides exemplary performance in ensuring that the CO2 is removed sufficiently and the ventilation flow is adequate for maintaining CO2 washout in the AEMU spacesuit helmet of the crew member during an EVA. This paper will review the recent developments of the RCA unit, testing planned in-house with a spacesuit simulator, and the associated analytical work along with insights from the medical aspect on the testing. 1

  3. Are physiotherapy graduates adequately prepared to to manage hiv/aids patients

    Directory of Open Access Journals (Sweden)

    T. Puckree

    2004-02-01

    Full Text Available Physiotherapy learners treat patients with Human Immuno-deficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS. There is no available published research on physiotherapy learners' opinions about how the South Afican physiotherapy undergraduate program is  helping them cope with HIV/AIDS patients. This study determines whether the physiotherapy degree offered at South African Universities, adequately prepares learners to cope with HIV/AIDS patients. Differences in knowledge and attitudes of physiotherapy learners regarding HIV/AIDS, amongst  universities is also explored. Two hundred and two senior physiotherapy learners from eight South African universities returned their  questionnaires and 55% of these were viable for analysis. A large portion (79% of learners indicated that the physiotherapy undergraduate degree did not adequately prepare them to cope with HIV/AIDS patients. Learners' knowledge and attitudes regarding HIV/AIDS differed significantly (41% to 73%  amongst universities. Formal lectures on HIV/AIDS significantly affected knowledge (0% -100% but not attitude towards patients. The role of the physiotherapist, precautions, transmission modes, syndrome stages, counseling and clinical skills were considered critical in the management of HIV/AIDS patients.

  4. 21 CFR 740.10 - Labeling of cosmetic products for which adequate substantiation of safety has not been obtained.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Labeling of cosmetic products for which adequate..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) COSMETICS COSMETIC PRODUCT WARNING STATEMENTS Warning Statements § 740.10 Labeling of cosmetic products for which adequate substantiation of safety has not...

  5. An Adequate Approach to Image Retrieval Based on Local Level Feature Extraction

    Directory of Open Access Journals (Sweden)

    Sumaira Muhammad Hayat Khan

    2010-10-01

    Full Text Available Image retrieval based on text annotation has become obsolete and is no longer interesting for scientists because of its high time complexity and low precision in results. Alternatively, increase in the amount of digital images has generated an excessive need for an accurate and efficient retrieval system. This paper proposes content based image retrieval technique at a local level incorporating all the rudimentary features. Image undergoes the segmentation process initially and each segment is then directed to the feature extraction process. The proposed technique is also based on image?s content which primarily includes texture, shape and color. Besides these three basic features, FD (Fourier Descriptors and edge histogram descriptors are also calculated to enhance the feature extraction process by taking hold of information at the boundary. Performance of the proposed method is found to be quite adequate when compared with the results from one of the best local level CBIR (Content Based Image Retrieval techniques.

  6. The classification of explosion-proof protected induction motor into adequate temperature and efficiency class

    Science.gov (United States)

    Brinovar, Iztok; Srpčič, Gregor; Seme, Sebastijan; Štumberger, Bojan; Hadžiselimović, Miralem

    2017-07-01

    This article deals with the classification of explosion-proof protected induction motors, which are used in hazardous areas, into adequate temperature and efficiency class. Hazardous areas are defined as locations with a potentially explosive atmosphere where explosion may occur due to present of flammable gasses, liquids or combustible dusts (industrial plants, mines, etc.). Electric motors and electrical equipment used in such locations must be specially designed and tested to prevent electrical initiation of explosion due to high surface temperature and arcing contacts. This article presents the basic tests of three-phase explosion-proof protected induction motor with special emphasis on the measuring system and temperature rise test. All the measurements were performed with high-accuracy instrumentation and accessory equipment and carried out at the Institute of energy technology in the Electric machines and drives laboratory and Applied electrical engineering laboratory.

  7. Adequate bases of phase space master integrals for $gg \\to h$ at NNLO and beyond

    CERN Document Server

    Höschele, Maik; Ueda, Takahiro

    2014-01-01

    We study master integrals needed to compute the Higgs boson production cross section via gluon fusion in the infinite top quark mass limit, using a canonical form of differential equations for master integrals, recently identified by Henn, which makes their solution possible in a straightforward algebraic way. We apply the known criteria to derive such a suitable basis for all the phase space master integrals in afore mentioned process at next-to-next-to-leading order in QCD and demonstrate that the method is applicable to next-to-next-to-next-to-leading order as well by solving a non-planar topology. Furthermore, we discuss in great detail how to find an adequate basis using practical examples. Special emphasis is devoted to master integrals which are coupled by their differential equations.

  8. Adequate bases of phase space master integrals for gg → h at NNLO and beyond

    Science.gov (United States)

    Höschele, Maik; Hoff, Jens; Ueda, Takahiro

    2014-09-01

    We study master integrals needed to compute the Higgs boson production cross section via gluon fusion in the infinite top quark mass limit, using a canonical form of differential equations for master integrals, recently identified by Henn, which makes their solution possible in a straightforward algebraic way. We apply the known criteria to derive such a suitable basis for all the phase space master integrals in afore mentioned process at next-to-next-to-leading order in QCD and demonstrate that the method is applicable to next-to-next-to-next-to-leading order as well by solving a non-planar topology. Furthermore, we discuss in great detail how to find an adequate basis using practical examples. Special emphasis is devoted to master integrals which are coupled by their differential equations.

  9. Adaptive robust image registration approach based on adequately sampling polar transform and weighted angular projection function

    Science.gov (United States)

    Wei, Zhao; Tao, Feng; Jun, Wang

    2013-10-01

    An efficient, robust, and accurate approach is developed for image registration, which is especially suitable for large-scale change and arbitrary rotation. It is named the adequately sampling polar transform and weighted angular projection function (ASPT-WAPF). The proposed ASPT model overcomes the oversampling problem of conventional log-polar transform. Additionally, the WAPF presented as the feature descriptor is robust to the alteration in the fovea area of an image, and reduces the computational cost of the following registration process. The experimental results show two major advantages of the proposed method. First, it can register images with high accuracy even when the scale factor is up to 10 and the rotation angle is arbitrary. However, the maximum scaling estimated by the state-of-the-art algorithms is 6. Second, our algorithm is more robust to the size of the sampling region while not decreasing the accuracy of the registration.

  10. Precise femtosecond laser ablation of dental hard tissue: preliminary investigation on adequate laser parameters

    Science.gov (United States)

    Hikov, Todor; Pecheva, Emilia; Montgomery, Paul; Antoni, Frederic; Leong-Hoi, Audrey; Petrov, Todor

    2017-01-01

    This work aims at evaluating the possibility of introducing state-of-the-art commercial femtosecond laser system in restorative dentistry by maintaining well-known benefits of lasers for caries removal, but also in overcoming disadvantages such as thermal damage of irradiated substrate. Femtosecond ablation of dental hard tissue is investigated by changing the irradiation parameters (pulsed laser energy, scanning speed and pulse repetition rate), assessed for enamel and dentin. The femtosecond laser system used in this work may be suitable for cavity preparation in dentin and enamel, due to the expected effective ablation and low temperature increase when using ultra short laser pulses. If adequate laser parameters are selected, this system seems to be promising for promoting a laser-assisted, minimally invasive approach in restorative dentistry.

  11. Overcome of Carbon Catabolite Repression of Bioinsecticides Production by Sporeless Bacillus thuringiensis through Adequate Fermentation Technology.

    Science.gov (United States)

    Ben Khedher, Saoussen; Jaoua, Samir; Zouari, Nabil

    2014-01-01

    The overcoming of catabolite repression, in bioinsecticides production by sporeless Bacillus thuringiensis strain S22 was investigated into fully controlled 3 L fermenter, using glucose based medium. When applying adequate oxygen profile throughout the fermentation period (75% oxygen saturation), it was possible to partially overcome the catabolite repression, normally occurring at high initial glucose concentrations (30 and 40 g/L glucose). Moreover, toxin production yield by sporeless strain S22 was markedly improved by the adoption of the fed-batch intermittent cultures technology. With 22.5 g/L glucose used into culture medium, toxin production was improved by about 36% when applying fed-batch culture compared to one batch. Consequently, the proposed fed-batch strategy was efficient for the overcome of the carbon catabolite repression. So, it was possible to overproduce insecticidal crystal proteins into highly concentrated medium.

  12. Overcome of Carbon Catabolite Repression of Bioinsecticides Production by Sporeless Bacillus thuringiensis through Adequate Fermentation Technology

    Directory of Open Access Journals (Sweden)

    Saoussen Ben Khedher

    2014-01-01

    Full Text Available The overcoming of catabolite repression, in bioinsecticides production by sporeless Bacillus thuringiensis strain S22 was investigated into fully controlled 3 L fermenter, using glucose based medium. When applying adequate oxygen profile throughout the fermentation period (75% oxygen saturation, it was possible to partially overcome the catabolite repression, normally occurring at high initial glucose concentrations (30 and 40 g/L glucose. Moreover, toxin production yield by sporeless strain S22 was markedly improved by the adoption of the fed-batch intermittent cultures technology. With 22.5 g/L glucose used into culture medium, toxin production was improved by about 36% when applying fed-batch culture compared to one batch. Consequently, the proposed fed-batch strategy was efficient for the overcome of the carbon catabolite repression. So, it was possible to overproduce insecticidal crystal proteins into highly concentrated medium.

  13. Nebulized antibiotics. An adequate option for treating ventilator-associated respiratory infection?

    Science.gov (United States)

    Rodríguez, A; Barcenilla, F

    2015-03-01

    Ventilator-associated tracheobronchitis (VAT) is a frequent complication in critical patients. The 90% of those who develop it receive broad-spectrum antibiotic (ATB) treatment, without any strong evidence of its favorable impact. The use of nebulized ATB could be a valid treatment option, to reduce the use of systemic ATB and the pressure of selection on the local flora. Several studies suggest that an adequate nebulization technique can ensure high levels of ATB even in areas of lung consolidation, and to obtain clinical and microbiological cure. New studies are needed to properly assess the impact of treatment with nebulized ATB on the emergence of resistance. Copyright © 2014 Elsevier España, S.L.U. y SEMICYUC. All rights reserved.

  14. Matching occupation and self: does matching theory adequately model children's thinking?

    Science.gov (United States)

    Watson, Mark; McMahon, Mary

    2004-10-01

    The present exploratory-descriptive cross-national study focused on the career development of 11- to 14-yr.-old children, in particular whether they can match their personal characteristics with their occupational aspirations. Further, the study explored whether their matching may be explained in terms of a fit between person and environment using Holland's theory as an example. Participants included 511 South African and 372 Australian children. Findings relate to two items of the Revised Career Awareness Survey that require children to relate personal-social knowledge to their favorite occupation. Data were analyzed in three stages using descriptive statistics, i.e., mean scores, frequencies, and percentage agreement. The study indicated that children perceived their personal characteristics to be related to their occupational aspirations. However, how this matching takes place is not adequately accounted for in terms of a career theory such as that of Holland.

  15. Adequate vitamin D status and adiposity contribute to bone health in peripubertal nonobese children.

    Science.gov (United States)

    Lee, Young Ah; Kim, Ji Young; Kang, Min Jae; Chung, Seung Joon; Shin, Choong Ho; Yang, Sei Won

    2013-05-01

    The dietary reference intake (DRI) of vitamin D for Korean children was reduced from 400 IU/day in 2005 to 200 IU/day in 2010. We evaluated the risk factors for low 25-hydroxyvitamin D [25(OH)D] status and its relationships with bone health in peripubertal nonobese children living in Seoul or Gyeonggi-do. One hundred children (9.3 ± 1.9 years, 71 prepubertal, 45 boys) participated in the winter (n = 38, December through March) and summer (June through September). Bone mineral content (Z_BMC), fat mass (Z_FM), lean mass (Z_LM), and bone mineral density for the total body (Z_TB) and lumbar spine (Z_L1-4) were measured using dual-energy X-ray absorptiometry. Twenty-nine percent of children (47.4 % in winter, 17.7 % in summer) were vitamin D deficient (25(OH)D level of vitamin D intake (P = 0.044) were associated with low 25(OH)D level. The 25(OH)D level correlated positively with Z_BMC (P = 0.040), Z_TB (P = 0.027), and Z_L1-4 (P = 0.045) independently of sex, puberty, Z_FM, Z_LM, physical activity level, and calcium intake. Z_FM correlated independently with Z_BMC (P vitamin D deficient in winter. Adequate vitamin D status and adiposity contributed to good bone health in nonobese children. Considering the beneficial effects of adequate vitamin D status on bone health, the current DRI may be insufficient for preventing vitamin D deficiency in winter among Korean children.

  16. Use of Linear Programming to Develop Cost-Minimized Nutritionally Adequate Health Promoting Food Baskets

    Science.gov (United States)

    Tetens, Inge; Dejgård Jensen, Jørgen; Smed, Sinne; Gabrijelčič Blenkuš, Mojca; Rayner, Mike; Darmon, Nicole; Robertson, Aileen

    2016-01-01

    Background Food-Based Dietary Guidelines (FBDGs) are developed to promote healthier eating patterns, but increasing food prices may make healthy eating less affordable. The aim of this study was to design a range of cost-minimized nutritionally adequate health-promoting food baskets (FBs) that help prevent both micronutrient inadequacy and diet-related non-communicable diseases at lowest cost. Methods Average prices for 312 foods were collected within the Greater Copenhagen area. The cost and nutrient content of five different cost-minimized FBs for a family of four were calculated per day using linear programming. The FBs were defined using five different constraints: cultural acceptability (CA), or dietary guidelines (DG), or nutrient recommendations (N), or cultural acceptability and nutrient recommendations (CAN), or dietary guidelines and nutrient recommendations (DGN). The variety and number of foods in each of the resulting five baskets was increased through limiting the relative share of individual foods. Results The one-day version of N contained only 12 foods at the minimum cost of DKK 27 (€ 3.6). The CA, DG, and DGN were about twice of this and the CAN cost ~DKK 81 (€ 10.8). The baskets with the greater variety of foods contained from 70 (CAN) to 134 (DGN) foods and cost between DKK 60 (€ 8.1, N) and DKK 125 (€ 16.8, DGN). Ensuring that the food baskets cover both dietary guidelines and nutrient recommendations doubled the cost while cultural acceptability (CAN) tripled it. Conclusion Use of linear programming facilitates the generation of low-cost food baskets that are nutritionally adequate, health promoting, and culturally acceptable. PMID:27760131

  17. Are general surgery residents adequately prepared for hepatopancreatobiliary fellowships? A questionnaire-based study

    Science.gov (United States)

    Osman, Houssam; Parikh, Janak; Patel, Shirali; Jeyarajah, D Rohan

    2015-01-01

    Background The present study was conducted to assess the preparedness of hepatopancreatobiliary (HPB) fellows upon entering fellowship, identify challenges encountered by HPB fellows during the initial part of their HPB training, and identify potential solutions to these challenges that can be applied during residency training. Methods A questionnaire was distributed to all HPB fellows in accredited HPB fellowship programmes in two consecutive academic years (n = 42). Reponses were then analysed. Results A total of 19 (45%) fellows responded. Prior to their fellowship, 10 (53%) were in surgical residency and the rest were in other surgical fellowships or surgical practice. Thirteen (68%) were graduates of university-based residency programmes. All fellows felt comfortable in performing basic laparoscopic procedures independently at the completion of residency and less comfortable in performing advanced laparoscopy. Eight (42%) fellows cited a combination of inadequate case volume and lack of autonomy during residency as the reasons for this lack of comfort. Thirteen (68%) identified inadequate preoperative workup and management as their biggest fear upon entering practice after general surgery training. A total of 17 (89%) fellows felt they were adequately prepared to enter HPB fellowship. Extra rotations in transplant, vascular or minimally invasive surgery were believed to be most helpful in preparing general surgery residents pursing HPB fellowships. Conclusions Overall, HPB fellows felt themselves to be adequately prepared for fellowship. Advanced laparoscopic procedures and the perioperative management of complex patients are two of the challenges facing HPB fellows. General surgery residents who plan to pursue an HPB fellowship may benefit from spending extra rotations on certain subspecialties. Focus on perioperative workup and management should be an integral part of residency and fellowship training. PMID:25387852

  18. Disparities in adequate mental health care for past-year major depressive episodes among Caucasian and Hispanic youths.

    Science.gov (United States)

    Alexandre, Pierre K; Martins, Silvia S; Richard, Patrick

    2009-10-01

    Following efforts made in recent years to provide effective mental health treatments based on evidence-based guidelines, a working definition was developed in the literature detailing a minimum level of "adequate mental health care" for serious mental illness. However, little is known about racial or ethnic disparities in receipt of adequate mental health care for individuals affected with serious mental illness. The objective of this study was to examine disparities among Caucasian and Hispanic youths in receipt of adequate mental health care for past-year major depressive episodes. Data for this study were drawn from the 2005 National Survey on Drug Use and Health. The study sample was composed of 1,169 Caucasian youths and 316 Hispanic youths aged 12 to 17 with past-year major depressive episodes. The percentages of youths in the sample who received adequate mental health care for past-year major depressive episodes were estimated, and the correlates of receipt of adequate mental health care were examined. Thirty-four percent of the full sample received adequate mental health care for past-year major depressive episodes, but separate analyses indicated that adequate mental health care was received by a significantly higher proportion of Caucasian youths (36%) than Hispanic youths (27%). The odds of receiving adequate mental health care for past-year major depressive episodes for Caucasians were 1.55 times that of Hispanics (p=.01). Having Medicaid or coverage via the State Children's Health Insurance Program significantly increased the odds of receiving adequate mental care for past-year major depressive episodes for both Hispanics and Caucasians. As mental health problems of adolescents from diverse racial or ethnic backgrounds become more easily identified and a larger proportion of these groups is referred to mental health treatment services, it is important to examine the degree to which treatment should be tailored to engage and retain specific racial or

  19. Virulence characteristics of Salmonella following deletion of genes encoding the tRNA modification enzymes GidA and MnmE.

    Science.gov (United States)

    Shippy, Daniel C; Eakley, Nicholas M; Lauhon, Charles T; Bochsler, Philip N; Fadl, Amin A

    2013-04-01

    Salmonella is an important foodborne pathogen causing major public health problems throughout the world due to the consumption of contaminated food. Our previous studies have shown that deletion of glucose-inhibited division (gidA) gene significantly altered Salmonella virulence in both in vitro and in vivo models of infection. In Escherichia coli, GidA and MnmE have been shown to modify several bacterial factors by a post-transcriptional mechanism to modify tRNA. Therefore, we hypothesize that GidA and MnmE complex together to modulate virulence genes in Salmonella using a similar mechanism. To test our hypothesis, and to examine the relative contribution of GidA and MnmE in modulation of Salmonella virulence, we constructed gidA and mnmE single mutants as well as a gidA mnmE double mutant strain of Salmonella. Results from the in vitro data displayed a reduction in growth, motility, intracellular replication, and invasion of T84 intestinal epithelial cells in the mutant strains compared to the wild-type Salmonella strain. The in vivo data showed a significant attenuation of the mutant strains as indicated by the induction of inflammatory cytokines and chemokines, as well as in the severity of histopathological lesions in the liver and spleen, compared to mice infected with the wild-type strain. Also, a significant increase in the LD50 was observed in mice infected with the mutant strains, and mice immunized with the mutants were protected against a lethal dose of wild-type Salmonella. A pull-down assay indicated that Salmonella GidA and MnmE bind together, and HPLC analysis revealed that deletion of gidA and/or mnmE altered Salmonella tRNA modification. Overall, the data suggest MnmE and GidA bind together and use a post-transcriptional mechanism to modify tRNA to regulate Salmonella pathogenesis.

  20. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria

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    Stadler Peter F

    2011-05-01

    Full Text Available Abstract Background The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution. Results The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys. Conclusion A strong reversed asymmetrical mutational constraint in the mitochondrial genome of

  1. Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2

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    Zhao Wei

    2010-09-01

    Full Text Available Abstract Background tRNase Z is the endonuclease that is responsible for the 3'-end processing of tRNA precursors, a process essential for tRNA 3'-CCA addition and subsequent tRNA aminoacylation. Based on their sizes, tRNase Zs can be divided into the long (tRNase ZL and short (tRNase ZS forms. tRNase ZL is thought to have arisen from a tandem gene duplication of tRNase ZS with further sequence divergence. The species distribution of tRNase Z is complex. Fungi represent an evolutionarily diverse group of eukaryotes. The recent proliferation of fungal genome sequences provides an opportunity to explore the structural and functional diversity of eukaryotic tRNase Zs. Results We report a survey and analysis of candidate tRNase Zs in 84 completed fungal genomes, spanning a broad diversity of fungi. We find that tRNase ZL is present in all fungi we have examined, whereas tRNase ZS exists only in the fungal phyla Basidiomycota, Chytridiomycota and Zygomycota. Furthermore, we find that unlike the Pezizomycotina and Saccharomycotina, which contain a single tRNase ZL, Schizosaccharomyces fission yeasts (Taphrinomycotina contain two tRNase ZLs encoded by two different tRNase ZL genes. These two tRNase ZLs are most likely localized to the nucleus and mitochondria, respectively, suggesting partitioning of tRNase Z function between two different tRNase ZLs in fission yeasts. The fungal tRNase Z phylogeny suggests that tRNase ZSs are ancestral to tRNase ZLs. Additionally, the evolutionary relationship of fungal tRNase ZLs is generally consistent with known phylogenetic relationships among the fungal species and supports tRNase ZL gene duplication in certain fungal taxa, including Schizosaccharomyces fission yeasts. Analysis of tRNase Z protein sequences reveals putative atypical substrate binding domains in most fungal tRNase ZSs and in a subset of fungal tRNase ZLs. Finally, we demonstrate the presence of pseudo-substrate recognition and catalytic motifs at

  2. The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?

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    Tate Warren

    2010-04-01

    Full Text Available Abstract Background Understanding the origin of protein synthesis has been notoriously difficult. We have taken as a starting premise Wolf and Koonin's view that "evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in an RNA world containing ribozymes with versatile activities". Presentation of the hypothesis We propose that coded protein synthesis arose from a noncoded process in an RNA world as a natural consequence of the accumulation of a range of early tRNAs and their serendipitous RNA binding partners. We propose that, initially, RNA molecules with 3' CCA termini that could be aminoacylated by ribozymes, together with an ancestral peptidyl transferase ribozyme, produced small peptides with random or repetitive sequences. Our concept is that the first tRNA arose in this context from the ligation of two RNA hairpins and could be similarly aminoacylated at its 3' end to become a substrate for peptidyl transfer catalyzed by the ancestral ribozyme. Within this RNA world we hypothesize that proto-mRNAs appeared first simply as serendipitous binding partners, forming complementary base pair interactions with the anticodon loops of tRNA pairs. Initially this may have enhanced stability of the paired tRNA molecules so they were held together in close proximity, better positioning the 3' CCA termini for peptidyl transfer and enhancing the rate of peptide synthesis. If there were a selective advantage for the ensemble through the peptide products synthesized, it would provide a natural pathway for the evolution of a coding system with the expansion of a cohort of different tRNAs and their binding partners. The whole process could have occurred quite unremarkably for such a profound acquisition. Testing the hypothesis It should be possible to test the different parts of our model using the isolated contemporary 50S ribosomal subunit initially, and then with RNAs

  3. Adequate sleep among adolescents is positively associated with health status and health-related behaviors

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    Jeng Yi-Jong

    2006-03-01

    Full Text Available Abstract Background Amount of sleep is an important indicator of health and well-being in children and adolescents. Adequate sleep (AS: adequate sleep is defined as 6–8 hours per night regularly is a critical factor in adolescent health and health-related behaviors. The present study was based on a health promotion project previously conducted on adolescents in Tao-Yuan County, Taiwan. The aim was to examine the relationship between AS during schooldays and excessive body weight, frequency of visiting doctors and health-related behaviors among Taiwanese adolescents. Methods A cross-sectional study design, categorical and multivariate data analyses were used. The hypotheses investigated were: high frequency of AS is positively associated with lack of obesity and less frequent visits to doctors; and high frequency AS is positively associated with health-related behavior. Results A total of 656 boys (53.2% and girls (46.8%, ranging in age from 13–18 years were studied between January and June 2004. Three hundred and fifty seven subjects (54% reported that they slept less than the suggested 6–8 hours on schooldays. A significant negative association was found between low sleep and of the following health-related behaviors: (1 life appreciation; (2 taking responsibility for health; (3 adopting healthy diet; (4 effective stress management; (5 regular exercise; and (6 total AHP score. High frequency AS was associated with low frequencies of obesity after potential confounding factors were controlled. Junior high school adolescents reported significantly higher frequencies of AS than high school participants. Gender, family structure, home location and frequency of television watching or computer use were not significantly associated with AS. Conclusion These findings support the proposition that AS is associated with good health status and high-frequency adoption of health-related behavior. Furthermore, these findings suggest that inadequate

  4. Leptin and its Receptors in Human Placenta of Small, Adequate, and Large for Gestational Age Newborns.

    Science.gov (United States)

    Lazo-de-la-Vega-Monroy, Maria-Luisa; González-Domínguez, Martha I; Zaina, Silvio; Sabanero, Myrna; Daza-Benítez, Leonel; Malacara, Juan Manuel; Barbosa-Sabanero, Gloria

    2017-05-01

    Alterations in birth weight impact postnatal outcome and adult metabolic health. Therefore, fetal growth regulation is crucial for preventing chronic metabolic diseases. Leptin has been suggested to play an important role in placental and fetal growth, albeit its specific mechanisms of action have not been elucidated. The aim of this study was to analyze leptin concentrations in placenta, cord blood, and maternal blood of SGA, AGA, and LGA (small, adequate and large for gestational age, respectively) newborns, as well as placental leptin receptor (LEPRa and LEPRb) protein expression. We performed a cross-sectional comparative study in 3 groups of healthy mothers and their term newborns at delivery (SGA, AGA, and LGA, n=20 per group). Placental, maternal blood, and cord blood leptin content were measured by ELISA. Placental LEPRa and LEPRb protein expression were determined by Western Blot. Maternal leptin concentrations correlated positively with maternal weight before and at the end of gestation, without differences between groups. Cord leptin is higher in LGA and lower in SGA, whereas placental leptin is higher in SGA. Placental leptin was inversely correlated with placental weight, independently from maternal weight and gestational age. Both LEPRa and LEPRb expression are lower in SGA, while LEPRa positively correlated with placental weight and birthweight. The current findings indicate that placental leptin and its receptors are differentially expressed in SGA, AGA, and LGA newborns. We suggest that placental leptin and LEPR protein expression may influence placental growth and thus, birth weight. © Georg Thieme Verlag KG Stuttgart · New York.

  5. Twenty-Four-Hour Urine Osmolality as a Physiological Index of Adequate Water Intake

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    Erica T. Perrier

    2015-01-01

    Full Text Available While associations exist between water, hydration, and disease risk, research quantifying the dose-response effect of water on health is limited. Thus, the water intake necessary to maintain optimal hydration from a physiological and health standpoint remains unclear. The aim of this analysis was to derive a 24 h urine osmolality (UOsm threshold that would provide an index of “optimal hydration,” sufficient to compensate water losses and also be biologically significant relative to the risk of disease. Ninety-five adults (31.5 ± 4.3 years, 23.2 ± 2.7 kg·m−2 collected 24 h urine, provided morning blood samples, and completed food and fluid intake diaries over 3 consecutive weekdays. A UOsm threshold was derived using 3 approaches, taking into account European dietary reference values for water; total fluid intake, and urine volumes associated with reduced risk for lithiasis and chronic kidney disease and plasma vasopressin concentration. The aggregate of these approaches suggest that a 24 h urine osmolality ≤500 mOsm·kg−1 may be a simple indicator of optimal hydration, representing a total daily fluid intake adequate to compensate for daily losses, ensure urinary output sufficient to reduce the risk of urolithiasis and renal function decline, and avoid elevated plasma vasopressin concentrations mediating the increased antidiuretic effort.

  6. An adequate interset rest period for strength recovery during a common isokinetic test.

    Science.gov (United States)

    Blazquez, Ivan N; Warren, Barbara L; O'Hanlon, Ann M; Silvestri, Lynette R

    2013-07-01

    Isokinetic testing is used in rehabilitation settings on a regular basis; yet, there is a lack of consistency in rest period usage among protocols. Furthermore, the allotment of rest periods has been arbitrary (e.g., 30, 60, 90 seconds or more). This investigation examines the work:rest ratio as an effective method of standardizing rest periods in isokinetic testing. The purpose of this study was to establish an adequate rest period that would allow reproducibility of strength during a common isokinetic strength test. Twenty-seven healthy college-aged men (age, 23 ± 3.8 years; body weight, 79.54 ± 11.09 kg) were tested on 5 separate occasions: 2 familiarization sessions and 3 experimental sessions. Each subject performed a knee extension/flexion isokinetic strength protocol (Cybex NORM; Lumex, Inc., Ronkonkoma, NY, USA) to determine peak torque by performing 5 maximal reciprocal repetitions at each ascending velocity of 60, 180, and 300°·s. Work:rest ratios of 1:3, 1:8, and 1:12 were counterbalanced between sets. A 3 × 3 repeated measures analysis of variance was used to analyze the data. A significance level of α ≤ 0.05 was used for all tests. There was no significant difference in either knee extension or knee flexion peak torque when comparing work:rest ratios. These findings suggest that a 1:3 work:rest ratio is sufficient during a common isokinetic strength test.

  7. Assessing pharmacokinetics of different doses of fosfomycin in laboratory rats enables adequate exposure for pharmacodynamic models.

    Science.gov (United States)

    Poeppl, Wolfgang; Lingscheid, Tilman; Bernitzky, Dominik; Donath, Oliver; Reznicek, Gottfried; Zeitlinger, Markus; Burgmann, Heinz

    2014-01-01

    Fosfomycin has been the subject of numerous pharmacodynamic in vivo models in recent years. The present study set out to determine fosfomycin pharmacokinetics in laboratory rats to enable adequate dosing regimens in future rodent models. Fosfomycin was given intraperitoneally as single doses of 75, 200 and 500 mg/kg bodyweight to 4 Sprague-Dawley rats per dose group. Blood samples were collected over 8 h and fosfomycin concentrations were determined by HPLC-mass spectrometry. Fosfomycin showed a dose-proportional pharmacokinetic profile indicated by a correlation of 0.99 for maximum concentration and area under the concentration-time curve (AUC). The mean AUC0-8 after intraperitoneal administration of 75, 200 or 500 mg/kg bodyweight fosfomycin were 109.4, 387.0 and 829.1 µg·h/ml, respectively. In conclusion, a dosing regimen of 200-500 mg/kg 3 times daily is appropriate to obtain serum concentrations in laboratory rats, closely mimicking human serum concentrations over time.

  8. Internship training adequately prepares South African medical graduates for community service - with exceptions.

    Science.gov (United States)

    Nkabinde, T C; Ross, A; Reid, S; Nkwanyana, N M

    2013-09-30

    The 2-year internship period for medical graduates began in South Africa in 2005 and has never been formally evaluated. This study assessed the perceptions of community service medical officers (COSMOs) working at district hospitals (DHs) in KwaZulu-Natal (KZN) to determine whether the 2-year internship programme had adequately prepared them for community service (CS). A cross-sectional descriptive study was conducted regarding the perceptions of COSMOs working at 22 district hospitals in KZN. Data were collected in July 2012, using a questionnaire based on the core skills and knowledge detailed in the Health Professions Council of South Africa intern log book. All eight domains were self-assessed and a score of 4 out of 5 indicated an ability to work independently. Of the COSMOs, 78% (60 out of 89) completed the questionnaire. Most felt well-prepared for CS in all disciplines, but critical gaps in knowledge and skills were identified in paediatrics, orthopaedics, anaesthetics and obstetrics. In addition, 75% of respondents (45 out of 60) expressed a need for additional training in the disciplines of ear, nose and throat (ENT), urology, ophthalmology and dermatology. The 2-year internship has provided the basis for independent medical practice in DHs. However, certain critical skill gaps need urgent attention, particularly in obstetrics and anaesthesia. Areas of weakness in ENT, urology, ophthalmology and dermatology could be addressed by including these specialities as a compulsory rotation in surgery, medicine or family medicine during internship training.

  9. Are Nutritional Care Adequate for Elderly Hospitalized Patients? A Cross-Sectional Study

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    Helene Kjøllesdal Eide

    2016-12-01

    Full Text Available This article assesses nutritional care in identifying and treating nutritional risk in elderly hospitalized patients. A cross-sectional study was conducted at a large Norwegian University hospital in the period 2011 to 2013. Data on nutritional risk and care for elderly patients (≥70 years without dementia were collected at 20 wards by 173 second-year nursing students in acute-care clinical studies. A stratified sampling technique was utilized to improve the representativeness of the sample. In total, 508 patients (48.8% women with a mean age of 79.6 years participated. The internationally and nationally recommended nutritional care was not implemented at the hospital, suggesting that nutritional care for elderly hospitalized patients was not adequate. This implies that the majority of the elderly patients nutritionally at risk are neither identified nor treated according to their needs. The article highlights the importance of having systematic nutritional care practices to make it possible for the hospital ward staff to routinely identify nutritional risk and initiate appropriate nutritional treatment measures.

  10. A high UV environment does not ensure adequate Vitamin D status

    Science.gov (United States)

    Kimlin, M. G.; Lang, C. A.; Brodie, A.; Harrison, S.; Nowak, M.; Moore, M. R.

    2006-12-01

    Queensland has the highest rates of skin cancer in the world and due to the high levels of solar UV in this region it is assumed that incidental UV exposure should provide adequate vitamin D status for the population. This research was undertaken to test this assumption among healthy free-living adults in south-east Queensland, Australia (27°S), at the end of winter. This research was approved by Queensland University of Technology Human Research Ethics Committee and conducted under the guidelines of the Declaration of Helsinki. 10.2% of the sample had serum vitamin D levels below 25nm/L (deficiency) and a further 32.3% had levels between 25nm/L and 50nm/L (insufficiency). Vitamin D deficiency and insufficiency can occur at the end of winter, even in sunny climates. The wintertime UV levels in south-east Queensland (UV index 4-6) are equivalent to summertime UV levels in northern regions of Europe and the USA. These ambient UV levels are sufficient to ensure synthesis of vitamin D requirements. We investigated individual UV exposure (through a self reported sun exposure questionnaire) and found correlations between exposure and Vitamin D status. Further research is needed to explore the interactions between the solar UV environment and vitamin D status, particularly in high UV environments, such as Queensland.

  11. Improved ASTM G72 Test Method for Ensuring Adequate Fuel-to-Oxidizer Ratios

    Science.gov (United States)

    Juarez, Alfredo; Harper, Susana Tapia

    2016-01-01

    The ASTM G72/G72M-15 Standard Test Method for Autogenous Ignition Temperature of Liquids and Solids in a High-Pressure Oxygen-Enriched Environment is currently used to evaluate materials for the ignition susceptibility driven by exposure to external heat in an enriched oxygen environment. Testing performed on highly volatile liquids such as cleaning solvents has proven problematic due to inconsistent test results (non-ignitions). Non-ignition results can be misinterpreted as favorable oxygen compatibility, although they are more likely associated with inadequate fuel-to-oxidizer ratios. Forced evaporation during purging and inadequate sample size were identified as two potential causes for inadequate available sample material during testing. In an effort to maintain adequate fuel-to-oxidizer ratios within the reaction vessel during test, several parameters were considered, including sample size, pretest sample chilling, pretest purging, and test pressure. Tests on a variety of solvents exhibiting a range of volatilities are presented in this paper. A proposed improvement to the standard test protocol as a result of this evaluation is also presented. Execution of the final proposed improved test protocol outlines an incremental step method of determining optimal conditions using increased sample sizes while considering test system safety limits. The proposed improved test method increases confidence in results obtained by utilizing the ASTM G72 autogenous ignition temperature test method and can aid in the oxygen compatibility assessment of highly volatile liquids and other conditions that may lead to false non-ignition results.

  12. Are GPs adequately equipped with the knowledge for educating and counseling of families with ADHD children?

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    Zarei Nabi

    2010-01-01

    Full Text Available Abstract Background Attention deficit hyperactivity disorder is one of the most common child psychiatry disorders. General physicians (GP, as primary care providers, can have an important role in screening and treatment of ADHD. This study aimed to survey GPs' knowledge, attitude, and their views of their role in the screening, diagnosing and managing children with ADHD. Methods Six hundred and sixty five general physicians in Shiraz, Iran, answered a self-reported questionnaire on ADHD. The questionnaire consisted of questions regarding socio-demographic characteristics such as age, the duration of practice as a GP, marital status, general knowledge about ADHD, and the management of ADHD. Results Less than half of them believed that they have adequate knowledge and information about this disorder. They usually do not like to be the primary care providers for children with ADHD. The majority of them prefer to refer the children to related specialists, mostly psychiatrists or psychologists. More than one third of them believed that sugar is a cause of ADHD. Only 6.6% of them reported that ADHD persists for the whole life. Their knowledge about methylphenidate is reasonable. Conclusions As many other countries worldwide, the knowledge of GPs about ADHD should be improved. They do not asses and manage children with probable ADHD by themselves without referring to related professionals. They do not opt for the use of methylphenidate.

  13. [Survey of Trichophyton tonsurans infection in Japan. Molecular epidemiology and factors affecting adequate hairbrush sampling].

    Science.gov (United States)

    Mochizuki, Takashi; Tanabe, Hiroshi; Wakasa, Asako; Kawasaki, Masako; Anzawa, Kazushi; Ishizaki, Hiroshi

    2006-01-01

    At the 48th Annual Meeting of The Society for Japanese Medical Mycology, held in October, 2004, we reported our findings from a survey on Trichophyton tonsurans infections in the Hokuriku and Kinki regions of Japan. The survey revealed that a few epidemics had occurred across these regions. In this article, we introduce our subsequent studies relating to 1) molecular epidemiology of isolates taken from people in many parts of Japan and 2) factors affecting adequate sampling of the scalp with hairbrushes, essential for surveying and monitoring the infection. In total, 198 isolates of Trichophyton tonsurans were analyzed using restriction fragment length polymorphisms of the non-transcribed spacer regions of ribosomal RNA genes. The restriction enzyme Mva I indicated two molecular types of strains, implying that the causative agents of the epidemic had different origins. None of the isolates obtained from the epidemic showed the same restriction profile as that of isolates from aged and sporadic cases. The published hairbrush method suitable for obtaining samples from the scalp of Judo trainees was reevaluated by changing several factors. We found that sampling should not be done soon after the students' physical training because other fungal elements may give a false positive, samples should not be obtained from students who have recently applied topical antimycotics, and samples should be taken under the guidance of qualified instructors familiar with the sampling method.

  14. Is current medical education adequately preparing future physicians to manage concussion: an initial evaluation.

    Science.gov (United States)

    Donaworth, Michael A; Grandhi, Ravi K; Logan, Kelsey; Gubanich, Paul J; Myer, Gregory D

    2016-01-01

    In 2010, there were 2.5 million hospitalizations, emergency room visits, or deaths associated with concussions in the United States.[1] Knowledge deficits exist among physicians regarding concussion management, which can lead to severe repercussions, including poor patient outcomes, poor patient satisfaction, and potential medical-legal issues. While concussion is a prevalent condition evaluated in the medical field, medical students continue to have a knowledge deficit regarding concussion diagnosis, prognosis, medical management, and return to play guidelines. Medical students from a mid-western medical school completed a survey on concussion diagnosis, prognosis, medical management, and return to play guidelines. The response rate was 40%. The data suggests that the vast majority of medical students are able to define concussion; however, most reported never having a lecture dedicated to concussion during medical school and also lacked clinical experience with acute concussion and post-concussive syndrome. There are clear areas of deficiency as noted by the inability of students to correctly identify symptoms and appropriate management of concussion. The current study indicates that at an individual, mid-western, top 50 medical school, current medical trainees may not be adequately educated to identify and manage concussion. Future research is warranted to determine the optimal guidelines to educate future physicians as it pertains to concussion diagnosis, management, prognosis, and return to play guidelines.

  15. Aurally-adequate time-frequency analysis for scattered sound in auditoria

    Science.gov (United States)

    Norris, Molly K.; Xiang, Ning; Kleiner, Mendel

    2005-04-01

    The goal of this work was to apply an aurally-adequate time-frequency analysis technique to the analysis of sound scattering effects in auditoria. Time-frequency representations were developed as a motivated effort that takes into account binaural hearing, with a specific implementation of interaural cross-correlation process. A model of the human auditory system was implemented in the MATLAB platform based on two previous models [A. Härmä and K. Palomäki, HUTear, Espoo, Finland; and M. A. Akeroyd, A. Binaural Cross-correlogram Toolbox for MATLAB (2001), University of Sussex, Brighton]. These stages include proper frequency selectivity, the conversion of the mechanical motion of the basilar membrane to neural impulses, and binaural hearing effects. The model was then used in the analysis of room impulse responses with varying scattering characteristics. This paper discusses the analysis results using simulated and measured room impulse responses. [Work supported by the Frank H. and Eva B. Buck Foundation.

  16. An RNA-binding complex involved in ribosome biogenesis contains a protein with homology to tRNA CCA-adding enzyme.

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    Jinzhong Lin

    2013-10-01

    Full Text Available A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins. Utp22 and Rrp7, two interacting proteins with no recognizable domain, are components of the 90S preribosome or the small subunit processome that conducts early processing of 18S rRNA. Here, we determine the cocrystal structure of Utp22 and Rrp7 complex at 1.97 Å resolution and the NMR structure of a C-terminal fragment of Rrp7, which is not visible in the crystal structure. The structure reveals that Utp22 surprisingly resembles a dimeric class I tRNA CCA-adding enzyme yet with degenerate active sites, raising an interesting evolutionary connection between tRNA and rRNA processing machineries. Rrp7 binds extensively to Utp22 using a deviant RNA recognition motif and an extended linker. Functional sites on the two proteins were identified by structure-based mutagenesis in yeast. We show that Rrp7 contains a flexible RNA-binding C-terminal tail that is essential for association with preribosomes. RNA-protein crosslinking shows that Rrp7 binds at the central domain of 18S rRNA and shares a neighborhood with two processing H/ACA snoRNAs snR30 and snR10. Depletion of snR30 prevents the stable assembly of Rrp7 into preribosomes. Our results provide insight into the evolutionary origin and functional context of Utp22 and Rrp7.

  17. Structural Basis for Fe-S Cluster Assembly and tRNA Thiolation Mediated by IscS Protein-Protein Interactions

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    Shi, Rong; Proteau, Ariane; Villarroya, Magda; Moukadiri, Ismaïl; Zhang, Linhua; Trempe, Jean-François; Matte, Allan; Armengod, M Eugenia; Cygler, Miroslaw [McGill; (LGM-Spain); (Biotech Res.)

    2010-05-04

    The cysteine desulfurase IscS is a highly conserved master enzyme initiating sulfur transfer via persulfide to a range of acceptor proteins involved in Fe-S cluster assembly, tRNA modifications, and sulfur-containing cofactor biosynthesis. Several IscS-interacting partners including IscU, a scaffold for Fe-S cluster assembly; TusA, the first member of a sulfur relay leading to sulfur incorporation into the wobble uridine of several tRNAs; ThiI, involved in tRNA modification and thiamine biosynthesis; and rhodanese RhdA are sulfur acceptors. Other proteins, such as CyaY/frataxin and IscX, also bind to IscS, but their functional roles are not directly related to sulfur transfer. We have determined the crystal structures of IscS-IscU and IscS-TusA complexes providing the first insight into their different modes of binding and the mechanism of sulfur transfer. Exhaustive mutational analysis of the IscS surface allowed us to map the binding sites of various partner proteins and to determine the functional and biochemical role of selected IscS and TusA residues. IscS interacts with its partners through an extensive surface area centered on the active site Cys328. The structures indicate that the acceptor proteins approach Cys328 from different directions and suggest that the conformational plasticity of a long loop containing this cysteine is essential for the ability of IscS to transfer sulfur to multiple acceptor proteins. The sulfur acceptors can only bind to IscS one at a time, while frataxin and IscX can form a ternary complex with IscU and IscS. Our data support the role of frataxin as an iron donor for IscU to form the Fe-S clusters.

  18. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes.

    Science.gov (United States)

    Ghosh, Amit; Vishveshwara, Saraswathi

    2008-11-04

    The allosteric concept has played a key role in understanding the biological functions of proteins. The rigidity or plasticity and the conformational population are the two important ideas invoked in explaining the allosteric effect. Although molecular insights have been gained from a large number of structures, a precise assessment of the ligand-induced conformational changes in proteins at different levels, ranging from gross topology to intricate details, remains a challenge. In this study, we have explored the conformational changes in the complexes of methionyl tRNA synthetase (MetRS) through novel network parameters such as cliques and communities, which identify the rigid regions in the protein structure networks (PSNs) constructed from the noncovalent interactions of amino acid side chains. MetRS belongs to the aminoacyl tRNA synthetase (aaRS) family that plays a crucial role in the translation of genetic code. These enzymes are modular with distinct domains from which extensive genetic, kinetic, and structural data are available, highlighting the role of interdomain communication. The network parameters evaluated here on the conformational ensembles of MetRS complexes, generated from molecular dynamics simulations, have enabled us to understand the interdomain communication in detail. Additionally, the characterization of conformational changes in terms of cliques and communities has also become possible, which had eluded conventional analyses. Furthermore, we find that most of the residues participating in cliques and communities are strikingly different from those that take part in long-range communication. The cliques and communities evaluated here for the first time on PSNs have beautifully captured the local geometries in detail within the framework of global topology. Here the allosteric effect is revealed at the residue level via identification of the important residues specific for structural rigidity and functional flexibility in MetRS. This ought

  19. Site-directed in vitro replacement of nucleosides in the anticodon loop of tRNA: application to the study of structural requirements for queuine insertase activity.

    Science.gov (United States)

    Carbon, P; Haumont, E; Fournier, M; de Henau, S; Grosjean, H

    1983-01-01

    We have investigated the specificity of the enzymes Q-insertase and mannosyl-Q transferase that replace the guanosine at position 34 (wobble base) in the anticodon of several tRNAs by Q or mannosyl-Q derivatives. We have restructured in vitro the normal anticodon of yeast tRNA-Asp-GUC, yeast tRNAArgICG and yeast tRNALeuUAG. With yeast tRNA-Asp-GUC, we have replaced one or several nucleotides in the vicinity of G34 by one of the four canonical nucleotides or by pseudouridylic acid; we have also constructed a tRNAAsp with eight bases instead of seven in the anticodon loop. With yeast tRNAArgICG and yeast tRNALeuUAG, we have replaced their anticodon by the trinucleotide GUC, coding for aspartic acid. The chimerical tRNAs were microinjected into the cytoplasm of Xenopus laevis oocytes and after 72 h the amount of Q34 and mannosyl-Q34 incorporated was measured. Our results show that the U33G34U35 sequence, within an anticodon loop of seven bases in chimerical yeast tRNA-Asp-GUC, tRNAArgGUC or tRNALeuGUC, is the main determinant for Q-insertase activity at position 34; the rest of the tRNA sequence has only a slight influence. For mannosyl-Q transferase, however, a much broader structural feature of the tRNA than just the U33G34U35 sequence is important for the efficiency of Q34 transformation into mannosyl-Q34.

  20. Determinants of prompt and adequate care among presumed malaria cases in a community in eastern Rwanda: A cross sectional study

    NARCIS (Netherlands)

    Ingabire, C.M.; Kateera, F.; Hakizimana, E.; Rulisa, A.; Muvunyi, C.; Mens, P.; Koenraadt, C.J.M.; Mutesa, L.; Vugt, M. van; Borne, B. van den; Alaii, J.

    2016-01-01

    Background: In order to understand factors influencing fever/malaria management practices among community-based individuals, the study evaluated psychosocial, socio-demographic and environmental determinants of prompt and adequate healthcare-seeking behaviours. Methods: A quantitative household (HH)

  1. Adequate image quality with reduced radiation dose in prospectively triggered coronary CTA compared with retrospective techniques

    Energy Technology Data Exchange (ETDEWEB)

    Arnoldi, Elisabeth; Johnson, Thorsten R.; Rist, Carsten; Wintersperger, Bernd J.; Sommer, Wieland H.; Becker, Christoph R.; Reiser, Maximilian F.; Nikolaou, Konstantin [Ludwig-Maximilians University, Department of Clinical Radiology, University Hospitals Munich - Grosshadern Campus, Munich (Germany); Becker, Alexander [Ludwig-Maximilians University, Department of Medicine I, University Hospitals Munich - Grosshadern Campus, Munich (Germany)

    2009-09-15

    The goal of our study was to compare a prospective triggering (PT) CT technique with retrospectively gated (RG) CT techniques in coronary computed tomographic angiograms (CCTA) with respect to image quality and radiation dose. Sixty consecutive patients were enrolled. CCTAs using the RG technique were obtained with a dual-source 64-slice CT system in 40 patients, using ECG-triggered tube current modulation, with either a broad pulsing window at 30-80% of the RR interval (group RGb, 20 patients, heart rate > 70 bpm) or a small pulsing window at 70% (group RGs, 20 patients, heart rate < 70 bpm). The other 20 patients underwent CCTA using the PT technique on a 128-slice CT system (group PT, heart rate < 70 bpm). All images were evaluated by two observers for quality on a three-point scale, with 1 being excellent and 3 being insufficient. The effective radiation dose was calculated for each patient. The average image quality score was 1.5 {+-} 0.6 for PT, 1.35 {+-} 0.5 for RGs and 1.65 {+-} 0.5 for RGb. The mean effective dose for RGb was 9 {+-} 4 mSv, for RGs 7 {+-} 3 mSv and for PT 3 {+-} 1 mSv. This represents a 57% dose reduction for PT compared with RGs and a 67% dose reduction for PT compared with RGb. In conclusion, in selected patients CCTA with the PT technique offers adequate image quality with a significantly lower radiation dose compared with CCTA using RG techniques. (orig.)

  2. Offering Adequate Pedagogical Progression via Mobile Equipments-Experiment of a French Engineering School

    Institute of Scientific and Technical Information of China (English)

    Jean-Luc Koning

    2006-01-01

    Students may enter our 5-year engineering school in France at two levels: first and third year.However, due to their quite different backgrounds (this is especially true for third year students), we need to provide newcomers with a 6-week training period during which they follow classes in the fields where they particularly feel weak. Unfortunately, depending on the student' s background, this is not always possible to bring him/her to the expected level. Another aspect one needs to mention is that these students may not have the same weaknesses in a given field. However, for economical reasons, those classes follow a uniform program as it is not feasible to provide a customized progression. In this paper we discuss how to redesign a mathematics course so as to offer tailored exercise sequencing.Groups of 20 students could then draw their exercises from an intranet database according to their previously completed work, try to solve it by themselves, request additional hints and even ask for some direct help from the teacher. Such a database is currently under development. If it turns out several students stumble against the same difficulty the teacher could show the whole class room how to solve it using the digital projector.This project goes one step further than our initial mobile education project ( 2003 ~ 2004 ). Until recently,we had used the equipment in a unique direction, from the instructor toward the students. Here, in this new project we are focusing on the whole loop in order to offer a more adequate (personalized) pedagogical progression: from the student to the teacher (when the tablet PCs are monitored by the teacher) , and back to-ward the students (when a direct help is proded by the teacher)

  3. Spirulina does not decrease muscle damage nor oxdidative stress in cycling athletes with adequate nutritional status

    Directory of Open Access Journals (Sweden)

    G.A.M. Franca

    2010-12-01

    Full Text Available The objective of this study was to assess the effect of Spirulina maxima on oxidative stress and muscle damage in cycling athletes subjected to high volume and intensity of training. Eighteen male athletes were randomly divided into an experimental group (n=11 with age 27.8±3.5 and placebo (n=7 with age 34.3±2.3 in a double-blind fashion. They carried out a protocol of Spirulina dietary supplementation (7.5 g/day of placebo for four weeks and maintained their trainings during this period. A nutritional anamnesis was performed and blood tests were done to determine pre and post levels of creatine kinase (CK, lactic dehydrogenase (LHD, superoxide dismutase (SOD and malondialdehyde (MDA. The supplemented and placebo groups performed the same volume training, has adequate macronutrients and antioxidant vitamins ingestion before study, as well as initial CK, LDH, SOD and MDA levels. Supplementation did not promote a significant alteration in CK levels on supplemented group (158.4±16.3 for 140.0±16.6 U/l, p>0.05, LDH (420±13.2 for 394.9±27.9 UI/l, p>0.05, MDA (2.8±0.2 for 2.9±0.4 nmol/ml, p>0.05, nor an increase in the SOD (7.3±0.6 for 7.0±0.6 U/mg Hb, p>0.05. We conclude that administration of Spirulina does not interfere in the magnitude of muscle damage nor in antioxidant status of cycling athletes that practice intense training.

  4. Emotional Experiences of Obese Women with Adequate Gestational Weight Variation: A Qualitative Study

    Science.gov (United States)

    Faria-Schützer, Débora Bicudo; Surita, Fernanda Garanhani de Castro; Alves, Vera Lucia Pereira; Vieira, Carla Maria; Turato, Egberto Ribeiro

    2015-01-01

    Background As a result of the growth of the obese population, the number of obese women of fertile age has increased in the last few years. Obesity in pregnancy is related to greater levels of anxiety, depression and physical harm. However, pregnancy is an opportune moment for the intervention of health care professionals to address obesity. The objective of this study was to describe how obese pregnant women emotionally experience success in adequate weight control. Methods and Findings Using a qualitative design that seeks to understand content in the field of health, the sample of subjects was deliberated, with thirteen obese pregnant women selected to participate in an individual interview. Data was analysed by inductive content analysis and includes complete transcription of the interviews, re-readings using suspended attention, categorization in discussion topics and the qualitative and inductive analysis of the content. The analysis revealed four categories, three of which show the trajectory of body care that obese women experience during pregnancy: 1) The obese pregnant woman starts to think about her body;2) The challenge of the diet for the obese pregnant woman; 3) The relation of the obese pregnant woman with the team of antenatal professionals. The fourth category reveals the origin of the motivation for the change: 4) The potentializing factors for change: the motivation of the obese woman while pregnant. Conclusions During pregnancy, obese women are more in touch with themselves and with their emotional conflicts. Through the transformations of their bodies, women can start a more refined self-care process and experience of the body-mind unit. The fear for their own and their baby's life, due to the risks posed by obesity, appears to be a great potentializing factor for change. The relationship with the professionals of the health care team plays an important role in the motivational support of the obese pregnant woman. PMID:26529600

  5. Ensuring Adequate Health and Safety Information for Decision Makers during Large-Scale Chemical Releases

    Science.gov (United States)

    Petropoulos, Z.; Clavin, C.; Zuckerman, B.

    2015-12-01

    The 2014 4-Methylcyclohexanemethanol (MCHM) spill in the Elk River of West Virginia highlighted existing gaps in emergency planning for, and response to, large-scale chemical releases in the United States. The Emergency Planning and Community Right-to-Know Act requires that facilities with hazardous substances provide Material Safety Data Sheets (MSDSs), which contain health and safety information on the hazardous substances. The MSDS produced by Eastman Chemical Company, the manufacturer of MCHM, listed "no data available" for various human toxicity subcategories, such as reproductive toxicity and carcinogenicity. As a result of incomplete toxicity data, the public and media received conflicting messages on the safety of the contaminated water from government officials, industry, and the public health community. Two days after the governor lifted the ban on water use, the health department partially retracted the ban by warning pregnant women to continue avoiding the contaminated water, which the Centers for Disease Control and Prevention deemed safe three weeks later. The response in West Virginia represents a failure in risk communication and calls to question if government officials have sufficient information to support evidence-based decisions during future incidents. Research capabilities, like the National Science Foundation RAPID funding, can provide a solution to some of the data gaps, such as information on environmental fate in the case of the MCHM spill. In order to inform policy discussions on this issue, a methodology for assessing the outcomes of RAPID and similar National Institutes of Health grants in the context of emergency response is employed to examine the efficacy of research-based capabilities in enhancing public health decision making capacity. The results of this assessment highlight potential roles rapid scientific research can fill in ensuring adequate health and safety data is readily available for decision makers during large

  6. Prevention of mother to child transmission lay counsellors: Are they adequately trained?

    Directory of Open Access Journals (Sweden)

    Catherine H. Thurling

    2012-05-01

    Full Text Available South Africa’s high prevalence of human immunodeficiency virus (HIV infected women requires a comprehensive health care approach to pregnancy because of the added risk of their HIV status. As a result of the shortage of health care workers in South Africa, lay counsellors play important roles in the prevention of mother to child transmission of HIV (PMTCT.There is no standardization of training of lay counsellors in South Africa, and training varies in length depending on the training organisation.The study aimed to investigate the training of lay counsellors by analysing their training curricula and interviewing lay counsellors about their perceptions of their training.A two phase research method was applied. Phase one documented an analysis of the training curricula. Phase two was semi-structured interviews with the participants. Purposive sampling was undertaken for this study. The total sample size was 13 people, with a final sample of 9 participants, determined at the point of data saturation.The research was qualitative, descriptive and contextual in design. The curricula analysed had different styles of delivery, and the approaches to learning and courses varied, resulting in inconsistent training outcomes. A need for supervision and mentorship in the working environment was also noted.The training of lay counsellors needs to be adapted to meet the extended roles that they are playing in PMTCT. The standardization of training programmes, and the incorporation of a system of mentorship in the work environment, would ensure that the lay counsellors are adequately prepared for their role in PMTCT.

  7. Do Foley catheters adequately drain the bladder? Evidence from CT imaging studies

    Energy Technology Data Exchange (ETDEWEB)

    Avulova, Svetlana; Li, Valery J.; Khusid, Johnathan A. [Department of Urology, SUNY Downstate College of Medicine, Brooklyn, NY (United States); Choi, Woo S. [Radiology, SUNY Downstate College of Medicine, Brooklyn, NY (United States); Weiss, Jeffrey P., E-mail: johnathan.khusid@downstate.edu [Department of Urology, Weill Cornell Medical College, New York, NY (United States)

    2015-05-15

    Introduction: The Foley catheter has been widely assumed to be an effective means of draining the bladder. However, recent studies have brought into question its efficacy. The objective of our study is to further assess the adequacy of Foley catheter for complete drainage of the bladder. Materials and Methods: Consecutive catheterized patients were identified from a retrospective review of contrast enhanced and non-contrast enhanced computed tomographic (CT) abdomen and pelvis studies completed from 7/1/2011-6/30/2012. Residual urine volume (RUV) was measured using 5mm axial CT sections as follows: The length (L) and width (W) of the bladder in the section with the greatest cross sectional area was combined with bladder height (H) as determined by multiplanar reformatted images in order to calculate RUV by applying the formula for the volume (V) of a sphere in a cube:V=(π/6)⁎L⁎W⁎H). Results: RUVs of 167 (mean age 67) consecutively catheterized men (n=72) and women (n=95) identified by CT abdomen and pelvis studies were calculated. The mean RUV was 13.2 mL (range: 0.0 mL-859.1 mL, standard deviation: 75.9 mL, margin of error at 95% confidence:11.6 mL). Four (2.4%) catheterized patients had RUVs of >50 mL, two of whom had an improperly placed catheter tip noted on their CT-reports. Conclusions: Previous studies have shown that up to 43% of catheterized patients had a RUV greater than 50 mL, suggesting inadequacy of bladder drainage via the Foley catheter. Our study indicated that the vast majority of patients with Foley catheters (97.6%), had adequately drained bladders with volumes of <50 mL. (author)

  8. Adequate levothyroxine doses for the treatment of hypothyroidism newly discovered during pregnancy.

    Science.gov (United States)

    Abalovich, Marcos; Vázquez, Adriana; Alcaraz, Graciela; Kitaigrodsky, Ariela; Szuman, Gabriela; Calabrese, Cristina; Astarita, Graciela; Frydman, Mario; Gutiérrez, Silvia

    2013-11-01

    Recent guidelines recommend thyrotropin (TSH) target levels of ≤2.5 mIU/L for the first trimester and ≤3 mIU/L for the subsequent trimesters. Euthyroidism should be attained as soon as possible, but there are no precise indications about the initial levothyrorine (LT4) dose. The aim of our study was to determine the appropriate LT4 doses in order to normalize TSH levels in patients with newly discovered subclinical hypothyroidism (SCH) during pregnancy, and to correlate them with basal TSH levels. The adequate LT4 doses for women with SCH were also compared to those required in pregnant women with overt hypothyroidism (OH). Seventy-seven patients with newly diagnosed hypothyroidism during pregnancy were retrospectively analyzed. Patients were assigned to group 1 (n = 64) with SCH or group 2 (n = 13) with OH. SCH patients were subdivided into two groups: group 1a serum TSH >2.5 (1st trimester) or >3 (2nd or 3rd trimester) to 4.2 mIU/L; and group 1b TSH level > 4.21-10 mIU/L. All patients were treated with LT4 as soon as hypothyroidism was diagnosed. The dose that allowed a TSH of ≤2.5 mIU/L to be reached in the first trimester or one that allowed a TSH of ≤3 mIU/L to be reached during the second and third trimesters was considered the appropriate one. A significant difference (p women with SCH and in 10/13 (76.92%) women with OH, the appropriate LT4 dose coincided with the initial dose. Only 11% and 23% respectively required additional adjustments. Once the appropriate dose of LT4 was prescribed, the time at which euthyroidism (mean ± SD, weeks) was confirmed was similar in patients with SCH (6.06 ± 3.3) and OH (5.3 ± 1.8). There were no miscarriages or premature deliveries. When hypothyroidism is newly discovered during pregnancy, we suggest initiating the treatment with the following LT4 doses: 1.20 μg/kg/day for SCH with TSH ≤ 4.2  mIU/L, 1.42 μg/kg/day with TSH > 4.2-10, and 2.33 μg/kg/day for OH. By taking this approach

  9. Global Uranium And Thorium Resources: Are They Adequate To Satisfy Demand Over The Next Half Century?

    Science.gov (United States)

    Lambert, I. B.

    2012-04-01

    This presentation will consider the adequacy of global uranium and thorium resources to meet realistic nuclear power demand scenarios over the next half century. It is presented on behalf of, and based on evaluations by, the Uranium Group - a joint initiative of the OECD Nuclear Energy Agency and the International Atomic Energy Agency, of which the author is a Vice Chair. The Uranium Group produces a biennial report on Uranium Resources, Production and Demand based on information from some 40 countries involved in the nuclear fuel cycle, which also briefly reviews thorium resources. Uranium: In 2008, world production of uranium amounted to almost 44,000 tonnes (tU). This supplied approximately three-quarters of world reactor requirements (approx. 59,000 tU), the remainder being met by previously mined uranium (so-called secondary sources). Information on availability of secondary sources - which include uranium from excess inventories, dismantling nuclear warheads, tails and spent fuel reprocessing - is incomplete, but such sources are expected to decrease in market importance after 2013. In 2008, the total world Reasonably Assured plus Inferred Resources of uranium (recoverable at less than 130/kgU) amounted to 5.4 million tonnes. In addition, it is clear that there are vast amounts of uranium recoverable at higher costs in known deposits, plus many as yet undiscovered deposits. The Uranium Group has concluded that the uranium resource base is more than adequate to meet projected high-case requirements for nuclear power for at least half a century. This conclusion does not assume increasing replacement of uranium by fuels from reprocessing current reactor wastes, or by thorium, nor greater reactor efficiencies, which are likely to ameliorate future uranium demand. However, progressively increasing quantities of uranium will need to be mined, against a backdrop of the relatively small number of producing facilities around the world, geopolitical uncertainties and

  10. 鸡硒蛋白T的硒代半胱氨酸插入序列元件、蛋白结构与功能及组织表达差异%Analysis of selenocysteine insertion sequence element, structures and functions and expression profiles of selenoprotein T in chicken

    Institute of Scientific and Technical Information of China (English)

    葛延松; 曹嫦妤; 王丽丽; 李楠; 江秀清; 李金龙

    2014-01-01

    应用生物软件分析鸡和其他11种脊椎动物硒蛋白 T ( selenoprotein T ,SelT )的硒代半胱氨酸插入序列( selenocysteine insertion sequence , SECIS)元件、SelT核苷酸和氨基酸序列的同源性,并分析鸡SelT 的结构及功能;采用实时荧光定量PCR( fluorescent quantitative real-time PCR , fqRT-PCR)方法检测SelT基因在35日龄鸡体内30种组织中的表达谱.结果显示:脊椎动物 SelT的SECIS元件均属于Ⅱ型结构;鸡 SelT核苷酸序列与其他11种脊椎动物的同源性在48.0%~85.1%之间,而氨基酸序列与非洲爪蟾、斑马鱼的同源性低于90.0%,与其他9种动物的同源性在90.6%~94.9%之间;鸡 SelT 属于跨膜蛋白,存在信号肽,属于 RDx 家族,酶活性分类为EC 2.5.1.18,具有氧化还原功能,且存在Ca2+结合位点.SelT在鸡各组织中广泛表达,在睾丸中含量极其丰富,提示鸡SelT在雄性生殖系统中可能发挥功能.%Selenium ( Se) was an important , biologically necessary trace element , which played an important biological roles in avian growth , reproduction , immune function and disease resistance . The biological significance of Se was attributed to its occurrence in selenoproteins in the form of selenocysteine ( Sec) with a 21 amino acid genetic code . Se uses the stop codon UGA as the coding codon encoding Sec . Selenoproteins involved in many life processes such as antioxidant defense , cell signal transduction , metabolic pathway , development , immune function , and hormone regulates , and it was related to the occurrence and mechanism of many diseases . Selenoprotein T (SelT) was originally identified through silico studies ,cloned and expressed in a mammalian cell line ,confirmed as a selenoprotein . Previous studies have proved that SelT mainly occurred in Golgi apparatus and endoplasmic reticulum , with important biological function . SelT can act on the Ca2+ homeostasis , involved in neuroendocrine secretion . SelT has

  11. Optimization of pharmacotherapy in chronic heart failure: is heart rate adequately addressed?

    Science.gov (United States)

    Franke, Jennifer; Wolter, Jan Sebastian; Meme, Lillian; Keppler, Jeannette; Tschierschke, Ramon; Katus, Hugo A; Zugck, Christian

    2013-01-01

    bpm (p <0.01). Likewise, comparing the groups ≥75 and <75 bpm, the primary endpoint was significantly increased in the group of patients with heart rates ≥75 bpm 27 vs. 12.2 %; p < 0.01). 5-year event-free survival was significantly lower among patients with heart rates ≥70 bpm as compared to those with <70 bpm (log-rank test p < 0.05) and among patients in the ≥75 bpm group versus <75 bpm group (log-rank test p < 0.01). In conclusion, in clinical practice, 53 % of CHF patients have inadequate heart rate control (heart rates ≥75 bpm) despite concomitant beta-blocker therapy. In this non-randomized cohort, adequate heart rate control under individually optimized beta-blocker therapy was associated with improved mid- and long-term clinical outcome up to 5 years. As further up titration of beta-blockers is not achievable in many patients, the administration of a selective heart rate lowering agent, such as ivabradine adjuvant to beta-blockers may pose an opportunity to further modulate outcome.

  12. Segmenting into Adequate Units for Automatic Recognition of Emotion-Related Episodes: A Speech-Based Approach

    Directory of Open Access Journals (Sweden)

    Anton Batliner

    2010-01-01

    Full Text Available We deal with the topic of segmenting emotion-related (emotional/affective episodes into adequate units for analysis and automatic processing/classification—a topic that has not been addressed adequately so far. We concentrate on speech and illustrate promising approaches by using a database with children's emotional speech. We argue in favour of the word as basic unit and map sequences of words on both syntactic and ‘‘emotionally consistent” chunks and report classification performances for an exhaustive modelling of our data by mapping word-based paralinguistic emotion labels onto three classes representing valence (positive, neutral, negative, and onto a fourth rest (garbage class.

  13. Developmental origins of metabolic disorders: The need for biomarker candidates and therapeutic targets from adequate preclinical models

    Directory of Open Access Journals (Sweden)

    Antonio Gonzalez-Bulnes

    2016-03-01

    Full Text Available The investigation on obesity and associated disorders have changed from an scenario in which genome drove the phenotype to a dynamic setup in which prenatal and early-postnatal conditions are determinant. However, research in human beings is difficult due to confounding factors (lifestyle and socioeconomic heterogeneity plus ethical issues. Hence, there is currently an intensive effort for developing adequate preclinical models, aiming for an adequate combination of basic studies in rodent models and specific preclinical studies in large animals. The results of these research strategies may increase the identification and development of contrasted biomarkers and therapeutic targets.

  14. New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures

    Directory of Open Access Journals (Sweden)

    Hotchkiss Graham

    2007-08-01

    Full Text Available Abstract Background In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development. We describe a transcriptomic and proteomic analysis of the effects of deleting bldA on cellular processes during submerged culture: conditions relevant to the industrial production of antibiotics. Results At the end of rapid growth, a co-ordinated transient up-regulation of about 100 genes, including many for ribosomal proteins, was seen in the parent strain but not the ΔbldA mutant. Increased basal levels of the signal molecule ppGpp in the mutant strain may be responsible for this difference. Transcripts or proteins from a further 147 genes classified as bldA-influenced were mostly expressed late in culture in the wild-type, though others were significantly transcribed during exponential growth. Some were involved in the biosynthesis of seven secondary metabolites; and some have probable roles in reorganising metabolism after rapid growth. Many of the 147 genes were "function unknown", and may represent unknown aspects of Streptomyces biology. Only two of the 147 genes contain a TTA codon, but some effects of bldA could be traced to TTA codons in regulatory genes or polycistronic operons. Several proteins were affected post-translationally by the bldA deletion. There was a statistically significant but weak positive global correlation between transcript and corresponding protein levels. Different technical limitations of the two approaches were a major cause of discrepancies in the results obtained with them. Conclusion Although deletion of bldA has very conspicuous effects on the gross phenotype, the bldA molecular phenotype revealed by the "dualomic" approach has shown that only about 2% of the genome is affected; but this includes many previously unknown effects at a variety of different levels, including post

  15. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse.

    Science.gov (United States)

    Darrow, Emily M; Chadwick, Brian P

    2014-06-01

    The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9-43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus.

  16. The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

    Science.gov (United States)

    Spencer, Mercedes; Wagner, Richard K.

    2017-01-01

    We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = -0.80), but these deficits were not as severe as their reading…

  17. Iodine Status of Women of Reproductive Age in Sierra Leone and Its Association with Household Coverage with Adequately Iodized Salt

    Directory of Open Access Journals (Sweden)

    Fabian Rohner

    2016-02-01

    Full Text Available Salt iodization programs are a public health success in tackling iodine deficiency. Yet, a large proportion of the world’s population remains at risk for iodine deficiency. In a nationally representative cross-sectional survey in Sierra Leone, household salt samples and women’s urine samples were quantitatively analyzed for iodine content. Salt was collected from 1123 households, and urine samples from 817 non-pregnant and 154 pregnant women. Household coverage with adequately iodized salt (≥15 mg/kg iodine was 80.7%. The median urinary iodine concentration (UIC of pregnant women was 175.8 µg/L and of non-pregnant women 190.8 µg/L. Women living in households with adequately iodized salt had higher median UIC (for pregnant women: 180.6 µg/L vs. 100.8 µg/L, respectively, p < 0.05; and for non-pregnant women: 211.3 µg/L vs. 97.8 µg/L, p < 0.001. Differences in UIC by residence, region, household wealth, and women’s education were much smaller in women living in households with adequately iodized salt than in households without. Despite the high household coverage of iodized salt in Sierra Leone, it is important to reach the 20% of households not consuming adequately iodized salt. Salt iodization has the potential for increasing equity in iodine status even with the persistence of other risk factors for deficiency.

  18. Using Fuzzy Logic to Identify Schools Which May Be Misclassified by the No Child Left Behind Adequate Yearly Progress Policy

    Science.gov (United States)

    Yates, Donald W.

    2009-01-01

    This investigation developed, tested, and prototyped a Fuzzy Inference System (FIS) that would assist decision makers in identifying schools that may have been misclassified by existing Adequate Yearly Progress (AYP) methods. This prototype was then used to evaluate Louisiana elementary schools using published school data for Academic Year 2004. …

  19. Are forestation, bio-char and landfilled biomass adequate offsets for the climate effects of burning fossil fuels?

    NARCIS (Netherlands)

    Reijnders, L.

    2009-01-01

    Forestation and landfilling purpose-grown biomass are not adequate offsets for the CO2 emission from burning fossil fuels. Their permanence is insufficiently guaranteed and landfilling purpose-grown biomass may even be counterproductive. As to permanence, bio-char may do better than forests or

  20. Fed up with the right to food? : The Netherlands' policies and practices regarding the human right to adequate food

    NARCIS (Netherlands)

    Hospes, O.; Meulen, van der B.M.J.

    2009-01-01

    There is no one in this world who would deny the importance of access to adequate food for every human being. In fact, access to food has been declared a human right in 1948 with the Universal Declaration of Human Rights. In spite of the right to food to be more than half a century old, many are not

  1. Using Fuzzy Logic to Identify Schools Which May Be Misclassified by the No Child Left Behind Adequate Yearly Progress Policy

    Science.gov (United States)

    Yates, Donald W.

    2009-01-01

    This investigation developed, tested, and prototyped a Fuzzy Inference System (FIS) that would assist decision makers in identifying schools that may have been misclassified by existing Adequate Yearly Progress (AYP) methods. This prototype was then used to evaluate Louisiana elementary schools using published school data for Academic Year 2004. …

  2. Fed up with the right to food? : The Netherlands' policies and practices regarding the human right to adequate food

    NARCIS (Netherlands)

    Hospes, O.; Meulen, van der B.M.J.

    2009-01-01

    There is no one in this world who would deny the importance of access to adequate food for every human being. In fact, access to food has been declared a human right in 1948 with the Universal Declaration of Human Rights. In spite of the right to food to be more than half a century old, many are not

  3. Are forestation, bio-char and landfilled biomass adequate offsets for the climate effects of burning fossil fuels?

    NARCIS (Netherlands)

    Reijnders, L.

    2009-01-01

    Forestation and landfilling purpose-grown biomass are not adequate offsets for the CO2 emission from burning fossil fuels. Their permanence is insufficiently guaranteed and landfilling purpose-grown biomass may even be counterproductive. As to permanence, bio-char may do better than forests or landf

  4. Assuring Adequate Health Insurance for Children With Special Health Care Needs: Progress From 2001 to 2009-2010.

    Science.gov (United States)

    Ghandour, Reem M; Comeau, Meg; Tobias, Carol; Dworetzky, Beth; Hamershock, Rose; Honberg, Lynda; Mann, Marie Y; Bachman, Sara S

    2015-01-01

    To report on coverage and adequacy of health insurance for children with special health care needs (CSHCN) in 2009-2010 and assess changes since 2001. Data were from the National Survey of Children with Special Health Care Needs (NS-CSHCN), a random-digit telephone survey with 40,243 (2009-2010) and 38,866 (2001) completed interviews. Consistency and adequacy of insurance was measured by: 1) coverage status, 2) gaps in coverage, 3) coverage of needed services, 4) reasonableness of uncovered costs, and 5) ability to see needed providers, as reported by parents. Bivariate and multivariable analyses were conducted to assess factors associated with adequate insurance coverage in 2009-2010. Unadjusted and adjusted prevalence estimates were examined to identify changes in the type of insurance coverage and the proportion of CSHCN with adequate coverage by insurance type. The proportion of CSHCN with private coverage decreased from 64.7% to 50.7% between 2001 and 2009-2010, while public coverage increased from 21.7% to 34.7%; the proportion of CSHCN without any insurance declined from 5.2% to 3.5%. The proportion of CSHCN with adequate coverage varied over time and by insurance type: among privately covered CSHCN, the proportion with adequate coverage declined (62.6% to 59.6%), while among publicly covered CSHCN, the proportion with adequate insurance increased (63.0% to 70.7%). Publicly insured CSHCN experienced improvements in each of the 3 adequacy components. There has been a continued shift from private to public coverage, which is more affordable, offers benefits that are more likely to meet CSHCN needs, and allowed CSHCN to see necessary providers. Published by Elsevier Inc.

  5. Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot–Marie–Tooth disease

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wei; Schimmel, Paul; Yang, Xiang-Lei, E-mail: xlyang@scripps.edu [Departments of Molecular Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States)

    2006-12-01

    Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot–Marie–Tooth Disease. Glycyl-tRNA synthetase (GlyRS) is one of a group of enzymes that catalyze the synthesis of aminoacyl-tRNAs for translation. Mutations of human and mouse GlyRSs are causally associated with Charcot–Marie–Tooth disease, the most common genetic disorder of the peripheral nervous system. As the first step towards a structure–function analysis of this disease, native human GlyRS was expressed, purified and crystallized. The crystal belonged to space group P4{sub 3}2{sub 1}2 or its enantiomorphic space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 91.74, c = 247.18 Å, and diffracted X-rays to 3.0 Å resolution. The asymmetric unit contained one GlyRS molecule and had a solvent content of 69%.

  6. Long-Range Structural Effects of a Charcot-Marie-Tooth Disease-Causing Mutation in Human Glycyl-TRNA Synthetase

    Energy Technology Data Exchange (ETDEWEB)

    Xie, W.; Nangle, L.A.; Zhang, W.; Schimmel, P.; Yang, X.-L.

    2009-06-04

    Functional expansion of specific tRNA synthetases in higher organisms is well documented. These additional functions may explain why dominant mutations in glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase cause Charcot-Marie-Tooth (CMT) disease, the most common heritable disease of the peripheral nervous system. At least 10 disease-causing mutant alleles of GlyRS have been annotated. These mutations scatter broadly across the primary sequence and have no apparent unifying connection. Here we report the structure of wild type and a CMT-causing mutant (G526R) of homodimeric human GlyRS. The mutation is at the site for synthesis of glycyl-adenylate, but the rest of the two structures are closely similar. Significantly, the mutant form diffracts to a higher resolution and has a greater dimer interface. The extra dimer interactions are located {approx}30 {angstrom} away from the G526R mutation. Direct experiments confirm the tighter dimer interaction of the G526R protein. The results suggest the possible importance of subtle, long-range structural effects of CMT-causing mutations at the dimer interface. From analysis of a third crystal, an appended motif, found in higher eukaryote GlyRSs, seems not to have a role in these long-range effects.

  7. Archaeal Tuc1/Ncs6 homolog required for wobble uridine tRNA thiolation is associated with ubiquitin-proteasome, translation, and RNA processing system homologs.

    Directory of Open Access Journals (Sweden)

    Nikita E Chavarria

    Full Text Available While cytoplasmic tRNA 2-thiolation protein 1 (Tuc1/Ncs6 and ubiquitin-related modifier-1 (Urm1 are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U at wobble uridines of tRNAs in eukaryotes, the biocatalytic roles and properties of Ncs6/Tuc1 and its homologs are poorly understood. Here we present the first report of an Ncs6 homolog of archaea (NcsA of Haloferax volcanii that is essential for maintaining cellular pools of thiolated tRNA(LysUUU and for growth at high temperature. When purified from Hfx. volcanii, NcsA was found to be modified at Lys204 by isopeptide linkage to polymeric chains of the ubiquitin-fold protein SAMP2. The ubiquitin-activating E1 enzyme homolog of archaea (UbaA was required for this covalent modification. Non-covalent protein partners that specifically associated with NcsA were also identified including UbaA, SAMP2, proteasome activating nucleotidase (PAN-A/1, translation elongation factor aEF-1α and a β-CASP ribonuclease homolog of the archaeal cleavage and polyadenylation specificity factor 1 family (aCPSF1. Together, our study reveals that NcsA is essential for growth at high temperature, required for formation of thiolated tRNA(LysUUU and intimately linked to homologs of ubiquitin-proteasome, translation and RNA processing systems.

  8. 人类线粒体tRNA生物合成与线粒体疾病%Human Mitochondrial tRNA Synthesis and Mitochondrial Diseases

    Institute of Scientific and Technical Information of China (English)

    阳娅玲; 肖红利; 管敏鑫

    2013-01-01

    线粒体是普遍存在于真核细胞中的一类细胞器.每个线粒体含有多个拷贝的闭合环状双链DNA.人类线粒体DNA (mitochondrial DNA,mtDNA)共编码22种线粒体tRNA(mitochondrial tRNA,mt tRNA),2种rRNA及13种多肽.mt tRNA独特的结构特点决定了它们与具有典型三叶草结构的细胞质tRNA不同.编码mt tRNA的基因突变频率较高,这可能是引起线粒体功能障碍的主要原因之一.同时,这与很多病理现象相关.目前发现,大量与mt tRNA生物代谢和功能相关的核因子包括加工内切酶、tRNA修饰酶和氨酰-tRNA合成酶.这些核因子的异常导致了疾病相关的tRNA致病突变.由此可见mt tRNA功能对于线粒体活性的重要性.

  9. Near-UV stress in salmonella typhimurium: 4-thiouridine in tRNA, ppGpp, and ApppGpp as components of an adaptive response

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, G.F.; Baker, J.C.; Ames, B.N.

    1988-05-01

    We have examined the role of 4-thiouridine in the responses of Salmonella typhimurium to near-UV irradiation. Mutants lacking 4-thiouridine (nuv) and mutants defective in the synthesis of ppGpp (guanosine 5'-diphosphate-3'-diphosphate) (relA) were found to be sensitive to killing by near-UV. Near-UV induced the synthesis of a set of proteins that were not induced in the nuv mutant. Some of these proteins were identified as oxidative defense proteins, and others were identified as ppGpp-inducible proteins. Over 100-fold increases in ApppGpp (adenoisine 5', 5'''-triphosphoguanosine-3'''-diphosphate, the adenylylated form of ppGpp) were observed in wild-type cells after near-UV irradiation but not in the 4-thiouridine-deficient mutant. These data support a model in which ppGpp and ApppGpp, a dinucleotide proposed to be synthesized by tRNA-aminoacyl synthetases as a response to the cross-linking of 4-thiouridine in tRNA by near-UV, induce the synthesis of proteins necessary for resistance to near-UV irradiation.

  10. Iodine Status of Women of Reproductive Age in Sierra Leone and Its Association with Household Coverage with Adequately Iodized Salt.

    Science.gov (United States)

    Rohner, Fabian; Wirth, James P; Woodruff, Bradley A; Chiwile, Faraja; Yankson, Hannah; Sesay, Fatmata; Koroma, Aminata S; Petry, Nicolai; Pyne-Bailey, Solade; Dominguez, Elisa; Kupka, Roland; Hodges, Mary H; de Onis, Mercedes

    2016-02-03

    Salt iodization programs are a public health success in tackling iodine deficiency. Yet, a large proportion of the world's population remains at risk for iodine deficiency. In a nationally representative cross-sectional survey in Sierra Leone, household salt samples and women's urine samples were quantitatively analyzed for iodine content. Salt was collected from 1123 households, and urine samples from 817 non-pregnant and 154 pregnant women. Household coverage with adequately iodized salt (≥15 mg/kg iodine) was 80.7%. The median urinary iodine concentration (UIC) of pregnant women was 175.8 µg/L and of non-pregnant women 190.8 µg/L. Women living in households with adequately iodized salt had higher median UIC (for pregnant women: 180.6 µg/L vs. 100.8 µg/L, respectively, p iodine status even with the persistence of other risk factors for deficiency.

  11. The Leap of a Provincial SME into the Global Market Using E-commerce: The Success of Adequate Planning

    Science.gov (United States)

    Sainz de Abajo, Beatriz; García Salcines, Enrique; Burón Fernández, F. Javier; López Coronado, Miguel; de Castro Lozano, Carlos

    The leap into the global market is not easy when it involves a provincial family business. This article demonstrates how adequate planning is fundamental in a small and medium-sized enterprise (SME) with the tight budget they have available to them, in order to be able to differentiate themselves in a highly competitive market, taking into accounts the benefits and risks involved. The Information Technology (IT) tools put in place will give the necessary support and allow for the possibility of increasing and improving the infrastructure as the company requires. An adequate strategy for the future to increases sales would be e-marketing techniques as well as the current promotions which contribute to diffusing the brand.

  12. Thermodynamic study and modelling of iron-based melts for adequate prediction of modern ladle metallurgy processes

    Science.gov (United States)

    Zaitsev, A. I.; Rodionova, I. G.; Shaposhnikov, N. G.; Zemlyanko, O. A.; Karamisheva, N. A.

    2008-02-01

    The representation of iron-based melts as associated liquids have been developed basing on the detail experimental investigation and analysis of available data on their thermodynamic properties and phase equilibria. It has allowed, for the first time, to interpret adequately the reactivity of the earth metals in the iron-based melts and to predict with high precision the reactions of metal refinement and non-metallic inclusions modifying in modern ladle metallurgy.

  13. The Audit Opinion of the DISA FY 2011 Working Capital Fund Financial Statements Was Not Adequately Supported

    Science.gov (United States)

    2013-04-26

    President’s Council on Integrity and Efficiency MD&A Management Discussion and Analysis MFR Memorandum for Record NoF Notification of...memorandums for record ( MFRs ) would have a material impact on the financial statements and ultimately Acuity’s opinion, • perform adequate completeness...the deficiencies identified by DISA in its FBWT MFRs would impact the reliability of the financial statements and ultimately Acuity’s opinion

  14. Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph.

    Science.gov (United States)

    Zauner, S; Fraunholz, M; Wastl, J; Penny, S; Beaton, M; Cavalier-Smith, T; Maier, U G; Douglas, S

    2000-01-04

    Cells of several major algal groups are evolutionary chimeras of two radically different eukaryotic cells. Most of these "cells within cells" lost the nucleus of the former algal endosymbiont. But after hundreds of millions of years cryptomonads still retain the nucleus of their former red algal endosymbiont as a tiny relict organelle, the nucleomorph, which has three minute linear chromosomes, but their function and the nature of their ends have been unclear. We report extensive cryptomonad nucleomorph sequences (68.5 kb), from one end of each of the three chromosomes of Guillardia theta. Telomeres of the nucleomorph chromosomes differ dramatically from those of other eukaryotes, being repeats of the 23-mer sequence (AG)(7)AAG(6)A, not a typical hexamer (commonly TTAGGG). The subterminal regions comprising the rRNA cistrons and one protein-coding gene are exactly repeated at all three chromosome ends. Gene density (one per 0.8 kb) is the highest for any cellular genome. None of the 38 protein-coding genes has spliceosomal introns, in marked contrast to the chlorarachniophyte nucleomorph. Most identified nucleomorph genes are for gene expression or protein degradation; histone, tubulin, and putatively centrosomal ranbpm genes are probably important for chromosome segregation. No genes for primary or secondary metabolism have been found. Two of the three tRNA genes have introns, one in a hitherto undescribed location. Intergenic regions are exceptionally short; three genes transcribed by two different RNA polymerases overlap their neighbors. The reported sequences encode two essential chloroplast proteins, FtsZ and rubredoxin, thus explaining why cryptomonad nucleomorphs persist.

  15. Do clinical examination gloves provide adequate electrical insulation for safe hands-on defibrillation? I: Resistive properties of nitrile gloves.

    Science.gov (United States)

    Deakin, Charles D; Lee-Shrewsbury, Victoria; Hogg, Kitwani; Petley, Graham W

    2013-07-01

    Uninterrupted chest compressions are a key factor in determining resuscitation success. Interruptions to chest compression are often associated with defibrillation, particularly the need to stand clear from the patient during defibrillation. It has been suggested that clinical examination gloves may provide adequate electrical resistance to enable safe hands-on defibrillation in order to minimise interruptions. We therefore examined whether commonly used nitrile clinical examination gloves provide adequate resistance to current flow to enable safe hands-on defibrillation. Clinical examination gloves (Kimberly Clark KC300 Sterling nitrile) worn by members of hospital cardiac arrest teams were collected immediately following termination of resuscitation. To determine the level of protection afforded by visually intact gloves, electrical resistance across the glove was measured by applying a DC voltage across the glove and measuring subsequent resistance. Forty new unused gloves (control) were compared with 28 clinical (non-CPR) gloves and 128 clinical (CPR) gloves. One glove in each group had a visible tear and was excluded from analysis. Control gloves had a minimum resistance of 120 kΩ (median 190 kΩ) compared with 60 kΩ in clinical gloves (both CPR (median 140 kΩ) and non-CPR groups (median 160 kΩ)). Nitrile clinical examination gloves do not provide adequate electrical insulation for the rescuer to safely undertake 'hands-on' defibrillation and when exposed to the physical forces of external chest compression, even greater resistive degradation occurs. Further work is required to identify gloves suitable for safe use for 'hands-on' defibrillation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. Subjects with molecularly defined familial hypercholesterolemia or familial defective apoB-100 are not being adequately treated.

    Directory of Open Access Journals (Sweden)

    Trond P Leren

    Full Text Available OBJECTIVES: To study whether subjects with a molecular genetic diagnosis of familial hypercholesterolemia (FH or familial defective apoB-100 (FDB are being adequately treated. DESIGN: A questionnaire regarding medical history was sent to 2611 subjects who had been provided with a molecular genetic diagnosis of FH or FDB, and a blood sample was obtained for lipid measurements. RESULTS: 956 (36.6% of the 2611 subjects participated. The mean age for starting lipid-lowering therapy was 33.4 (±12.1 years. Among those below 18 years of age, only 20.4% were on lipid-lowering drugs, whereas 89.1% of those aged 18 and above were on lipid-lowering drugs. The mean levels of total serum cholesterol and LDL-cholesterol were 5.7 (±1.5 mmol/l and 3.9 (±1.3 mmol/l, respectively. Among those who were on lipid-lowering drugs, 29.0% and 12.2% had levels of LDL cholesterol below 3.0 mmol/l and 2.6 mmol/l, respectively. Only 47.3% of the 956 subjects were considered as being adequately treated largely due to a failure to titrate their drug regimens. From the use of cholesterol-years score, lipid-lowering therapy must start before the age of 20 in order to prevent the subjects from contracting premature coronary heart disease. CONCLUSION: The majority of FH/FDB subjects are being diagnosed late in life and are not being adequately treated. In order to prevent them from contracting premature coronary heart disease, it is key that levels of LDL cholesterol are normalized from a young age and that sufficient doses of lipid-lowering drugs are being used.

  17. Combination of the somatic cell nuclear transfer method and RNAi technology for the production of a prion gene-knockdown calf using plasmid vectors harboring the U6 or tRNA promoter.

    Science.gov (United States)

    Wongsrikeao, Pimprapar; Sutou, Shizuyo; Kunishi, Miho; Dong, Ya Juan; Bai, Xuejin; Otoi, Takeshige

    2011-01-01

    By combining RNAi technology with SCNT method, we attempted to produce transgenic calves with knocked down bPRNP for technological assessments. The respective utilities of type II (tRNA) and type III (hU6) Pol III promoters in mediating plasmid vector-based RNAi for the production of a bPRNP-knockdown calf were compared. Plasmid harboring DNA for siRNA expression was introduced stably into the genome of primary cultured bovine cells. By inserting the transgenic cell into an enucleated bovine egg, SCNT embryos were produced. The ability for SCNT embryos to develop to blastocysts was higher in hU6 based vector groups (44-53%) than in a tRNA group (32%). In all, 30 hU6-embryos and 12 tRNA-embryos were transferred to 11 recipients. Only tRNA-embryos were able to impregnate recipients (6 out of 11 transfers), resulting in four aborted fetuses, one stillbirth, and one live-born calf. The expression of EGFP, a marker, was detected in all six. The bPRNP transcript levels in the nervous tissues (brain, cerebellum, spinal bulb, and spinal cord) from the calf, which was killed 20 days after birth, were reduced to 35% of those of the control calf on average, as determined by qRT-PCR. The PrPC levels, as estimated by western blot were reduced to 86% on average in the nervous tissues. These findings suggest that SCNT technology remains immature, that the tRNA promoter is useful, and that RNAi can significantly reduce PRNP mRNA levels, but insufficient reduction of PrPC levels exists in cattle under these conditions.

  18. Phentolamine as a treatment for poor mixing in transposition of the great arteries with adequate intraatrial communication.

    Science.gov (United States)

    Galal, M O; El-Naggar, W I; Sharfi, M H

    2005-01-01

    Patients with transposition of the great arteries often show poor mixing for different reasons, even after adequate balloon atrial septostomy. We present a patient with such a lesion whose clinical status improved dramatically after phentolamine was applied. We believe this improvement is due to reduction in afterload caused by the alpha(2) blocker and also possibly as a response to a presumptive effect of the drug on the diastolic function of the right ventricle, allowing more left-to-right shunt across the atrial septal defect. Both phenomena can improve cardiac output in such a situation.

  19. Study of the interactions between avian myeloblastosis virus reverse transcriptase and primer tRNA. Affinity labeling and inactivation of the enzyme by periodate-treated tRNATrp.

    OpenAIRE

    1980-01-01

    Reverse transcriptase from avian myeloblastosis virus can react with periodate-treated primer tRNATrp (beef) to form a Schiff's base between an epsilon-NH2 lysine group within the active center of the enzyme and the dialdehyde derivative of the 3' terminal ribose of tRNA. In the presence of cyanoborohydride the reversible imminium moiety of the Schiff's base is reduced to a more stable adduct. Non-primer tRNAs were not able to reduce the extent of primer fixation to the enzyme. Complete inact...

  20. Selenium and selenocysteine: roles in cancer, health, and development.

    Science.gov (United States)

    Hatfield, Dolph L; Tsuji, Petra A; Carlson, Bradley A; Gladyshev, Vadim N

    2014-03-01

    The many biological and biomedical effects of selenium are relatively unknown outside the selenium field. This fascinating element, initially described as a toxin, was subsequently shown to be essential for health and development. By the mid-1990s selenium emerged as one of the most promising cancer chemopreventive agents, but subsequent human clinical trials yielded contradictory results. However, basic research on selenium continued to move at a rapid pace, elucidating its many roles in health, development, and in cancer prevention and promotion. Dietary selenium acts principally through selenoproteins, most of which are oxidoreductases involved in diverse cellular functions.

  1. Routine supplementation does not warrant the nutritional status of vitamin D adequate after gastric bypass Roux-en-Y

    Directory of Open Access Journals (Sweden)

    Cintia Leticia da Rosa

    2013-02-01

    Full Text Available Bariatric surgery can lead to nutritional deficiencies, including those related to bone loss. The aim of this study was to evaluate serum concentrations of calcium, vitamin D and PTH in obese adults before and six months after gastric bypass surgery in Roux-en-Y (RYGB and evaluate the doses of calcium and vitamin D supplementation after surgery. Methods: Retrospective longitudinal study of adult patients of both sexes undergoing RYGB. We obtained data on weight, height, BMI and serum concentrations of 25-hydroxyvitamin D, ionized calcium and PTH. Following surgery, patients received dietary supplementation daily 500 mg calcium carbonate and 400 IU vitamin D. Results: We studied 56 women and 27 men. Preoperative serum concentrations of vitamin D were inadequate in 45% of women and 37% of men, while in the postoperative period 91% of women and 85% of men had deficiency of this vitamin. No change in serum calcium was found before and after surgery. Serum PTH preoperatively remained adequate in 89% of individuals of both sexes. After surgery serum concentrations remained adequate and 89% women and 83% men evaluated. Conclusion: Obesity appears to be a risk factor for the development of vitamin D. The results show that supplementation routine postoperative was unable to treat and prevent vitamin D deficiency in obese adults undergoing RYGB.

  2. Readiness to adopt adequate postural habits: an application of the Transtheoretical Model in the context of back pain prevention.

    Science.gov (United States)

    Keller, S; Herda, C; Ridder, K; Basler, H D

    2001-02-01

    Based on a biomechanical model, an adequate body posture can contribute to the prevention of back pain and back pain chronicity. This study examines the explanatory value of the Transtheoretical Model (TTM) for the adoption of adequate postural habits in a cross-sectional sample of 149 employees of a German administration unit (mean age 40.2 years, 50% female). Using newly developed instruments with satisfactory psychometric properties, basic assumptions of the TTM could be confirmed: self-efficacy and the perceived pros for maintaining a good body posture increased significantly across the stages, while the perceived cons decreased. Additionally, the use of preventive strategies for back pain prevention increased linearly and significantly across the stages of change. The study supports the applicability of the TTM for postural behavior. Considering stages of change as an intervening variable may contribute to clarifying the relationship between participation in low back schools and prevention of back pain chronicity. Longitudinal and intervention study data are needed to support these assumptions.

  3. Adequate Vitamin D Intake but Low Serum Levels in Pediatric Asthma Patients: A Pilot Study, Alberta Children’s Hospital

    Directory of Open Access Journals (Sweden)

    Sarah Howe McKenna

    2016-01-01

    Full Text Available Background. We assessed vitamin D intakes and serum 25(OH vitamin D levels in pediatric asthma patients on moderate-to-high dose inhaled steroids and compared them to published findings of healthy children in our city. Methods. Parents and/or patients were interviewed to estimate the children’s vitamin D intakes from foods and supplements (using an adapted validated food frequency questionnaire and asthma duration and management. Vitamin D status: serum 25-hyroxy vitamin D (25(OHD was obtained from the medical records. Results. Vitamin D intakes from food and supplements of the asthma patients (n=20, 742 ± 185 IU/day were significantly higher compared to healthy Canadian children (n=1442, 229 ± 121 IU/day. Despite higher vitamin D intakes, the children had nonsignificantly lower serum 25(OH vitamin D levels compared to the comparison group. Serum 25(OHD levels increased by 3.6 nmol/L with each 100 IU of vitamin D intake (95% Confidence interval = 2.0–4.0, R2 = 0.931, and p=0.001. Conclusion. Since adequate vitamin D status in asthma patients is necessary to support bone mineral accretion, it is important to achieve adequate vitamin D status by checking serum 25(OHD status and supplement accordingly.

  4. Exercise prescription for the older population: The interactions between physical activity, sedentary time, and adequate nutrition in maintaining musculoskeletal health.

    Science.gov (United States)

    Shad, Brandon J; Wallis, Gareth; van Loon, Luc J C; Thompson, Janice L

    2016-11-01

    Regular physical activity (PA) promotes musculoskeletal health in older adults. However, the majority of older individuals do not meet current PA guidelines and are also highly sedentary. Emerging evidence indicates that large amounts of sedentary time accelerate the loss of skeletal muscle mass (i.e., sarcopenia) and physical function with advancing age. However, current PA recommendations for sedentary time are non-specific (i.e., keep sedentary time to a minimum). Research indicates that physical inactivity and large amounts of sedentary time accelerate sarcopenic muscle loss by inducing skeletal muscle 'anabolic resistance'. These findings suggest a critical interaction between engaging in 'sufficient' levels of PA, minimising sedentary time, and consuming 'adequate' nutrition to promote optimal musculoskeletal health in older adults. However, current PA recommendations do not take into account the important role that nutrition plays in ensuring older adults can maximise the benefits from the PA in which they engage. The aim of this narrative review is: (1) to briefly summarise the evidence used to inform current public health recommendations for PA and sedentary time in older adults; and (2) to discuss the presence of 'anabolic resistance' in older adults, highlighting the importance of regular PA and minimising sedentary behaviour. It is imperative that the synergy between PA, minimising sedentary behaviour and adequate nutrition is integrated into future PA guidelines to promote optimal musculoskeletal health and metabolic responses in the growing ageing population.

  5. Median Urinary Iodine Concentrations Are Indicative of Adequate Iodine Status among Women of Reproductive Age in Prey Veng, Cambodia.

    Science.gov (United States)

    Karakochuk, Crystal D; Michaux, Kristina D; Chai, Tze L; Chan, Benny B; Whitfield, Kyly C; Barr, Susan I; McLean, Judy; Talukder, Aminuzzaman; Hou, Kroeun; Ly, Sokhoing; Green, Tim J

    2016-03-03

    Iodine deficiency disorders are estimated to affect over 1.9 million people worldwide. Iodine deficiency is especially serious for women during pregnancy and lactation because of the negative consequences for both mother and infant. The aim of this cross-sectional study was to determine the median urinary iodine concentration (UIC) as a population-level indicator of iodine status among rural women farmers of reproductive age (18-45 years) in the province of Prey Veng, Cambodia. A total of 450 women provided a spot morning urine sample in 2012. Of those women, 93% (n = 420) were non-pregnant and 7% (n = 30) were pregnant at the time of collection. UIC was quantified using the Sandell-Kolthoff reaction with modifications. The median UIC of non-pregnant (139 μg/L) and pregnant women (157 μg/L) were indicative of adequate iodine status using the WHO/UNICEF/ICCIDD epidemiological criteria for both groups (median UIC between 100-199 and 150-249 μg/L, respectively). We conclude that non-pregnant and pregnant women in rural Prey Veng, Cambodia had adequate iodine status based on single spot morning urine samples collected in 2012. More research is warranted to investigate iodine status among larger and more representative populations of women in Cambodia, especially in light of recent policy changes to the national program for universal salt iodization.

  6. Median Urinary Iodine Concentrations Are Indicative of Adequate Iodine Status among Women of Reproductive Age in Prey Veng, Cambodia

    Directory of Open Access Journals (Sweden)

    Crystal D. Karakochuk

    2016-03-01

    Full Text Available Iodine deficiency disorders are estimated to affect over 1.9 million people worldwide. Iodine deficiency is especially serious for women during pregnancy and lactation because of the negative consequences for both mother and infant. The aim of this cross-sectional study was to determine the median urinary iodine concentration (UIC as a population-level indicator of iodine status among rural women farmers of reproductive age (18–45 years in the province of Prey Veng, Cambodia. A total of 450 women provided a spot morning urine sample in 2012. Of those women, 93% (n = 420 were non-pregnant and 7% (n = 30 were pregnant at the time of collection. UIC was quantified using the Sandell-Kolthoff reaction with modifications. The median UIC of non-pregnant (139 μg/L and pregnant women (157 μg/L were indicative of adequate iodine status using the WHO/UNICEF/ICCIDD epidemiological criteria for both groups (median UIC between 100–199 and 150–249 μg/L, respectively. We conclude that non-pregnant and pregnant women in rural Prey Veng, Cambodia had adequate iodine status based on single spot morning urine samples collected in 2012. More research is warranted to investigate iodine status among larger and more representative populations of women in Cambodia, especially in light of recent policy changes to the national program for universal salt iodization.

  7. Vigorous cleaning and adequate ventilation are necessary to control an outbreak in a neonatal intensive care unit.

    Science.gov (United States)

    Shimono, Nobuyuki; Hayashi, Jun; Matsumoto, Hiroko; Miyake, Noriko; Uchida, Yujiro; Shimoda, Shinji; Furusyo, Norihiro; Akashi, Koichi

    2012-06-01

    An outbreak of Bacillus cereus (B. cereus) bacteremia occurred in our neonatal intensive care unit (NICU) in July 2005. Many strains of B. cereus were cultured from patient specimens, as well as from environmental samples such as the surfaces of instruments and air in the NICU. Some of these strains were analyzed by pulsed field gel electrophoresis, and several were confirmed to be identical. We speculated that the bacterial load in the environment had initially increased and then possibly spread throughout the NICU facility via the airflow of the ventilation system. For this reason, besides maintaining standard precautions, we performed a vigorous clean of the NICU, and covered the vents to prevent dust falling from them. These protective measures ended the outbreak. In the hospital environment, adequate ventilation is important, especially in single-occupancy isolation rooms and operating theaters. However, the criteria for the adequate ventilation of multioccupancy rooms for acute care environments such as the NICU have not yet been defined. We need to pay more attention to these environmental factors in order to avoid cross contamination and infectious outbreaks.

  8. [The global and national context regarding the challenges involved in ensuring adequate access to water for human consumption].

    Science.gov (United States)

    Augusto, Lia Giraldo da Silva; Gurgel, Idê Gomes Dantas; Câmara Neto, Henrique Fernandes; de Melo, Carlos Henrique; Costa, André Monteiro

    2012-06-01

    The scope of this article is to analyze the challenges involved in ensuring access to water for human consumption taking the international and national context into consideration. Based on the UN declaration that access to safe and clean drinking water is a fundamental human right, vulnerabilities are identified that can consist in restrictions to access to adequate supplies. The distribution of water and the population across the planet, pollution, inadequate policies and management lead to environmental injustice. The iniquity of access to water constitutes the contemporary water crisis. From the 1980s onwards, the transnational water market emerged for private control that occurs at three main levels: surface and underground water sources; bottled water; and public water supply services. The conflicts of the multiple uses of water resources, the market and environmental problems have contributed to rendering the health of the population and ecosystems vulnerable. Adequate public policies are essential to ensure the basic human right to access to safe and clean drinking water.

  9. The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation.

    Science.gov (United States)

    Aubee, Joseph I; Olu, Morenike; Thompson, Karl M

    2016-05-01

    The translation of rpoS(σ(S)), the general stress/stationary phase sigma factor, is tightly regulated at the post-transcriptional level by several factors via mechanisms that are not clearly defined. One of these factors is MiaA, the enzyme necessary for the first step in theN(6)-isopentyl-2-thiomethyl adenosinemethyl adenosine 37 (ms(2)i(6)A37) tRNA modification. We tested the hypothesis that an elevated UUX-Leucine/total leucine codon ratio can be used to identify transcripts whose translation would be sensitive to loss of the MiaA-dependent modification. We identified iraPas another candidate MiaA-sensitive gene, based on the UUX-Leucine/total leucine codon ratio. AniraP-lacZ fusion was significantly decreased in the abse nce of MiaA, consistent with our predictive model. To determine the role of MiaA in UUX-Leucine decoding in rpoS and iraP, we measured β-galactosidase-specific activity of miaA(-)rpo Sandira P translational fusions upon overexpression of leucine tRNAs. We observed suppression of the MiaA effect on rpoS, and notira P, via overexpression of tRNA(LeuX)but not tRNA(LeuZ) We also tested the hypothesis that the MiaA requirement for rpoS and iraP translation is due to decoding of UUX-Leucine codons within the rpoS and iraP transcripts, respectively. We observed a partial suppression of the MiaA requirement for rpoS and iraP translational fusions containing one or both UUX-Leucine codons removed. Taken together, this suggests that MiaA is necessary for rpoS and iraP translation through proper decoding of UUX-Leucine codons and that rpoS and iraP mRNAs are both modification tunable transcripts (MoTTs) via the presence of the modification.

  10. The Pai-associated leuX specific tRNA5(Leu) affects type 1fimbriation in pathogenic Escherichia coli by control of FimB recombinase expression

    DEFF Research Database (Denmark)

    Ritter, A.; Gally, D.; Olsen, Peter Bjarke

    1997-01-01

    of leuX. fimB transcription was influenced by thepresence of leuX, but only slightly affected by the presence or absence of leuX codons in fimB.FimB translation was significantly higher from codon-replaced fimB genes than that of wild-typefimB genes in various strain backgrounds. The fim switch was shown...... recognized by tRNA5Leu, fimE contains only two. It was proposed thatturning on the fim switch requires efficient translation of FimB, in turn requiring tRNA5Leu. Strainsin which the TTG codons in fimB were replaced with CTG codons at the wild-type locus were ableto produce type 1 fimbriae in the absence...... to be switched off inleuX-derivatives of E. coli 536, but could be found in the on position when the codon-altered fimBgene was exchanged into the chromosome of these strains. From these data, it is apparent thattRNA5Leu is required for efficient translation of FimB, in turn, leading to type 1 fimbrial...

  11. Peptidyl transferase antibiotics perturb the relative positioning of the 3'-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome

    DEFF Research Database (Denmark)

    Kirillov, S V; Porse, B T; Garrett, R A

    1999-01-01

    A range of antibiotic inhibitors that act within the peptidyl transferase center of the ribosome were examined for their capacity to perturb the relative positioning of the 3' end of P/P'-site-bound tRNA and the Escherichia coli ribosome. The 3'-terminal adenosines of deacylated tRNA and N......-Ac-Phe-tRNA were derivatized at the 2 position with an azido group and the tRNAs were cross-linked to the ribosome on irradiation with ultraviolet light at 365 nm. The cross-links were localized on the rRNA within extended versions of three previously characterized 23S rRNA fragments F1', F2', and F4......' at nucleotides C2601/A2602, U2584/U2585 (F1'), U2506 (F2'), and A2062/C2063 (F4'). Each of these nucleotides lies within the peptidyl transferase loop region of the 23S rRNA. Cross-links were also formed with ribosomal proteins L27 (strong) and L33 (weak), as shown earlier. The antibiotics sparsomycin...

  12. Enzymatic replacement in vitro of the first anticodon base of yeast tRNAAsp: application to the study of tRNA maturation in vivo, after microinjection into frog oocytes.

    Science.gov (United States)

    Carbon, P; Haumont, E; De Henau, S; Keith, G; Grosjean, H

    1982-06-25

    A combination of several enzymes, RNase-T1, nuclease S1, T4-polynucleotide kinase and T4-RNA ligase were used to prepare and modify different fragments of yeast tRNAAsp (normal anticodon G U C). This allowed us to reconstitute, in vitro, a chimeric tRNA that has any of the four bases G, A, U or C, as the first anticodon nucleotide, labelled with (32p) in its 3' position. Such reconstituted (32p) labelled yeast tRNAAsp were microinjected into the cytoplasm or the nucleus of the frog oocyte and checked for their stability as well as for their potential to work as a substrate for the maturation (modifying) enzymes under in vivo conditions. Our results indicate that the chimeric yeast tRNAsAsp were quite stable inside the frog oocyte. Also, the G34 was effectively transformed inside the cytoplasm of frog oocyte into Q34 and mannosyl-Q34; U34 into mcm5s2U and mcm5U. In contrast, C34 and A34 were not transformed at all neither in the cytoplasm nor in the nucleus of the frog oocyte. The above procedure constitutes a new approach in order to detect the presence of a given modifying enzyme inside the frog oocyte; also it provides informations about its cellular location and possibility about its specificity of interaction with foreign tRNA.

  13. Poor neurological sequelae of herpes simplex virus encephalitis in an infant despite adequate antiviral and adjunct corticosteroid therapy

    Directory of Open Access Journals (Sweden)

    Ratna B Basak

    2011-01-01

    Full Text Available A 2-month-old infant presented to our emergency department with fever, altered consciousness, and focal seizures of acute onset. He had vesicular skin lesions over the right preauricular region. CT brain showed a large hypodense lesion involving the left temporo-parietal region, left basal ganglia and left thalamus. MRI brain revealed bilateral multifocal corticomedullary lesions suggestive of encephalitis. CSF-PCR was positive for herpes simplex virus (HSV type I. He was treated with standard dose intravenous acyclovir for 15 days along with a trial of pulse methylprednisolone, but was readmitted within a week with features of an early relapse. The infant survived but developed significant neurological sequelae. Although treatment of HSV is available, the neurological outcome is guarded even with adequate antiviral therapy. Adjunct corticosteroid therapy did not appear to attenuate the neurological sequelae.

  14. Precise ablation of dental hard tissues with ultra-short pulsed lasers. Preliminary exploratory investigation on adequate laser parameters.

    Science.gov (United States)

    Bello-Silva, Marina Stella; Wehner, Martin; Eduardo, Carlos de Paula; Lampert, Friedrich; Poprawe, Reinhart; Hermans, Martin; Esteves-Oliveira, Marcella

    2013-01-01

    This study aimed to evaluate the possibility of introducing ultra-short pulsed lasers (USPL) in restorative dentistry by maintaining the well-known benefits of lasers for caries removal, but also overcoming disadvantages, such as thermal damage of irradiated substrate. USPL ablation of dental hard tissues was investigated in two phases. Phase 1--different wavelengths (355, 532, 1,045, and 1,064 nm), pulse durations (picoseconds and femtoseconds) and irradiation parameters (scanning speed, output power, and pulse repetition rate) were assessed for enamel and dentin. Ablation rate was determined, and the temperature increase measured in real time. Phase 2--the most favorable laser parameters were evaluated to correlate temperature increase to ablation rate and ablation efficiency. The influence of cooling methods (air, air-water spray) on ablation process was further analyzed. All parameters tested provided precise and selective tissue ablation. For all lasers, faster scanning speeds resulted in better interaction and reduced temperature increase. The most adequate results were observed for the 1064-nm ps-laser and the 1045-nm fs-laser. Forced cooling caused moderate changes in temperature increase, but reduced ablation, being considered unnecessary during irradiation with USPL. For dentin, the correlation between temperature increase and ablation efficiency was satisfactory for both pulse durations, while for enamel, the best correlation was observed for fs-laser, independently of the power used. USPL may be suitable for cavity preparation in dentin and enamel, since effective ablation and low temperature increase were observed. If adequate laser parameters are selected, this technique seems to be promising for promoting the laser-assisted, minimally invasive approach.

  15. Vegetable dishes, dairy products and fruits are key items mediating adequate dietary intake for Japanese adults with spinal cord injury.

    Science.gov (United States)

    Tsunoda, N; Inayama, T; Hata, K; Oka, J

    2015-11-01

    This is a cross-sectional study. The objective of this study was to ascertain the essential items mediating adequate dietary intake based on the Japanese Food Guide in common among the transtheoretical model (TTM), self-efficacy (SE) and outcome expectancy (OE). Members of the organization Spinal Injuries Japan. We posted a questionnaire survey to 2731 community-dwelling Japanese adults with spinal cord injury (SCI), and responses from 841 individuals were analyzed. Food intake was assessed as the frequency scores of 10 food items eaten in a daily diet in Japan. The correlations between the frequency scores of food intake and TTM, SE and OE were determined by binominal logistic regression analysis. The frequency scores of food intake were significantly associated with 'To eat vegetable dishes (dishes made mainly from vegetables or potatoes) not less than twice a day', 'To eat green/yellow vegetables not less than twice a day', 'To eat dairy products not less than once a day' and 'To eat fruits not less than once a day' in TTM. 'To eat vegetable dishes (dishes made mainly from vegetables or potatoes) not less than twice a day', 'To eat dairy products not less than once a day' and 'To eat fruits not less than once a day' were significantly associated with the frequency scores of food intake in SE. In OE, no differences were shown. This study finds that vegetable dishes, dairy products and fruits are the key items mediating adequate dietary intake. Dietary guidelines promoting the intake of these dishes for SCI individuals are needed.

  16. The two-layer geochemical structure of modern biogeochemical provinces and its significance for spatially adequate ecological evaluations and decisions

    Science.gov (United States)

    Korobova, Elena; Romanov, Sergey

    2014-05-01

    Contamination of the environment has reached such a scale that ecogeochemical situation in any area can be interpreted now as a result of the combined effect of natural and anthropogenic factors. The areas that appear uncomfortable for a long stay can have natural and anthropogenic genesis, but the spatial structure of such biogeochemical provinces is in any case formed of a combination of natural and technogenic fields of chemical elements. Features of structural organization and the difference in factors and specific time of their formation allow their separation on one hand and help in identification of areas with different ecological risks due to overlay of the two structures on the other. Geochemistry of soil cover reflects the long-term result of the naturally balanced biogeochemical cycles, therefore the soil geochemical maps of the undisturbed areas may serve the basis for evaluation of the natural geochemical background with due regard to the main factors of geochemical differentiation in biosphere. Purposeful and incidental technogenic concentrations and dispersions of chemical elements of specific (mainly mono- or polycentric) structure are also fixed in soils that serve as secondary sources of contamination of the vegetation cover and local food chains. Overlay of the two structures forms specific heterogeneity of modern biogeochemical provinces with different risk for particular groups of people, animals and plants adapted to specific natural geochemical background within particular concentration interval. The developed approach is believed to be helpful for biogeochemical regionalizing of modern biosphere (noosphere) and for spatially adequate ecogeochemical evaluation of the environment and landuse decisions. It allows production of a set of applied geochemical maps such as: 1) health risk due to chemical elements deficiency and technogenic contamination accounting of possible additive effects; 2) adequate soil fertilization and melioration with due

  17. Healthcare Costs Associated with an Adequate Intake of Sugars, Salt and Saturated Fat in Germany: A Health Econometrical Analysis.

    Science.gov (United States)

    Meier, Toni; Senftleben, Karolin; Deumelandt, Peter; Christen, Olaf; Riedel, Katja; Langer, Martin

    2015-01-01

    Non-communicable diseases (NCDs) represent not only the major driver for quality-restricted and lost life years; NCDs and their related medical treatment costs also pose a substantial economic burden on healthcare and intra-generational tax distribution systems. The main objective of this study was therefore to quantify the economic burden of unbalanced nutrition in Germany--in particular the effects of an excessive consumption of fat, salt and sugar--and to examine different reduction scenarios on this basis. In this study, the avoidable direct cost savings in the German healthcare system attributable to an adequate intake of saturated fatty acids (SFA), salt and sugar (mono- & disaccharides, MDS) were calculated. To this end, disease-specific healthcare cost data from the official Federal Health Monitoring for the years 2002-2008 and disease-related risk factors, obtained by thoroughly searching the literature, were used. A total of 22 clinical endpoints with 48 risk-outcome pairs were considered. Direct healthcare costs attributable to an unbalanced intake of fat, salt and sugar are calculated to be 16.8 billion EUR (CI95%: 6.3-24.1 billion EUR) in the year 2008, which represents 7% (CI95% 2%-10%) of the total treatment costs in Germany (254 billion EUR). This is equal to 205 EUR per person annually. The excessive consumption of sugar poses the highest burden, at 8.6 billion EUR (CI95%: 3.0-12.1); salt ranks 2nd at 5.3 billion EUR (CI95%: 3.2-7.3) and saturated fat ranks 3rd at 2.9 billion EUR (CI95%: 32 million-4.7 billion). Predicted direct healthcare cost savings by means of a balanced intake of sugars, salt and saturated fat are substantial. However, as this study solely considered direct medical treatment costs regarding an adequate consumption of fat, salt and sugars, the actual societal and economic gains, resulting both from direct and indirect cost savings, may easily exceed 16.8 billion EUR.

  18. Healthcare Costs Associated with an Adequate Intake of Sugars, Salt and Saturated Fat in Germany: A Health Econometrical Analysis.

    Directory of Open Access Journals (Sweden)

    Toni Meier

    Full Text Available Non-communicable diseases (NCDs represent not only the major driver for quality-restricted and lost life years; NCDs and their related medical treatment costs also pose a substantial economic burden on healthcare and intra-generational tax distribution systems. The main objective of this study was therefore to quantify the economic burden of unbalanced nutrition in Germany--in particular the effects of an excessive consumption of fat, salt and sugar--and to examine different reduction scenarios on this basis. In this study, the avoidable direct cost savings in the German healthcare system attributable to an adequate intake of saturated fatty acids (SFA, salt and sugar (mono- & disaccharides, MDS were calculated. To this end, disease-specific healthcare cost data from the official Federal Health Monitoring for the years 2002-2008 and disease-related risk factors, obtained by thoroughly searching the literature, were used. A total of 22 clinical endpoints with 48 risk-outcome pairs were considered. Direct healthcare costs attributable to an unbalanced intake of fat, salt and sugar are calculated to be 16.8 billion EUR (CI95%: 6.3-24.1 billion EUR in the year 2008, which represents 7% (CI95% 2%-10% of the total treatment costs in Germany (254 billion EUR. This is equal to 205 EUR per person annually. The excessive consumption of sugar poses the highest burden, at 8.6 billion EUR (CI95%: 3.0-12.1; salt ranks 2nd at 5.3 billion EUR (CI95%: 3.2-7.3 and saturated fat ranks 3rd at 2.9 billion EUR (CI95%: 32 million-4.7 billion. Predicted direct healthcare cost savings by means of a balanced intake of sugars, salt and saturated fat are substantial. However, as this study solely considered direct medical treatment costs regarding an adequate consumption of fat, salt and sugars, the actual societal and economic gains, resulting both from direct and indirect cost savings, may easily exceed 16.8 billion EUR.

  19. Structural and functional MRI study of the brain, cognition and mood in long-term adequately treated Hashimoto's thyroiditis.

    Science.gov (United States)

    Quinque, Eva M; Karger, Stefan; Arélin, Katrin; Schroeter, Matthias L; Kratzsch, Jürgen; Villringer, Arno

    2014-04-01

    The current study investigated neuropsychological and underlying structural and functional brain alterations in long-term adequately treated patients with Hashimoto's thyroiditis in order to examine much discussed residual complaints in patients in relation to possible long-term neural alterations with a specific interest in the underlying autoimmune process. Eighteen patients with treated hypothyroidism due to Hashimoto's thyroiditis (mean age 32, range 18-54 years; two males; mean treatment duration 4.4 years) and 18 healthy matched control subjects underwent 3-Tesla magnetic resonance imaging (MRI). Voxel-based morphometry was used to investigate grey matter density, resting-state functional MRI to analyse the brain connectivity of areas known to be altered in hypothyroidism and event-related functional MRI to examine brain activity during associative memory encoding. Neuropsychological assessment included memory, working memory, psychomotor speed and attention. We previously reported subclinically reduced mood in this study population and investigated its neural correlates here. Thyroid stimulating hormone, free triiodthyronine, free thyroxine and thyroid peroxidase antibodies were measured in serum. We did not find cognitive deficits or alterations in grey matter density, functional connectivity or associative memory-related brain activity in comparison to the control group and cognition was unrelated to thyroid serum measures in the patient group. Thyroid peroxidase antibodies in the patient group correlated with increased grey matter density in right amygdala and enhanced connectivity between subcallosal and parahippocampal areas. Treatment duration was associated with brain structure in frontal and occipital cortex and connectivity between left amygdala and frontal cortex. Mood correlated with brain areas associated with distinct functional networks, but not with those most prominently affected in depression. In conclusion, no cognitive or neural

  20. Adequately defining tumor cell proportion in tissue samples for molecular testing improves interobserver reproducibility of its assessment.

    Science.gov (United States)

    Lhermitte, Benoît; Egele, Caroline; Weingertner, Noëlle; Ambrosetti, Damien; Dadone, Bérengère; Kubiniek, Valérie; Burel-Vandenbos, Fanny; Coyne, John; Michiels, Jean-François; Chenard, Marie-Pierre; Rouleau, Etienne; Sabourin, Jean-Christophe; Bellocq, Jean-Pierre

    2017-01-01

    Gene mutation status assessment of tumors has become standard practice in diagnostic pathology. This is done using samples comprising tumor cells but also non-tumor cells, which may dramatically dilute the proportion of tumor DNA and induce false negative results. Increasing sensitivity of molecular tests presently allows detection of a targeted mutation in a sample with a small percentage of tumor cells, but assessment of tumor cellularity remains essential to adequately interpret the results of molecular tests. Comprehensive tumor cell counting would provide the most reliable approach but is time consuming, and therefore rough global estimations are used, the reliability of which has been questioned in view of their potential clinical impact. The French association for quality assurance in pathology (AFAQAP) conducted two external quality assurance schemes, partly in partnership with the French group of oncology cytogenomics (GFCO). The purpose of the schemes was to (1) evaluate how tumor cellularity is assessed on tissue samples, (2) identify reasons for discrepancies, and (3) provide recommendations for standardization and improvement. Tumor cell percentages in tissue samples of lung and colon cancer were estimated by 40-50 participants, on 10 H&E virtual slides and 20 H&E conventional slides. The average difference between lowest and highest estimated percentage was 66. This was largely due to inadequate definition of cellularity, reflecting confusion between the percentage of tumor cells and the percentage of the area occupied by tumor in the assessed region. The widest range of interobserver variation was observed for samples with dense or scattered lymphocytic infiltrates or with mucinous stroma. Estimations were more accurate in cases with a low percentage of tumor cells. Macrodissection of the most homogeneous area in the tissue reduced inter-laboratory variation. We developed a rating system indicating potential clinical impact of a discrepancy. Fewer

  1. Larger Thyroid Volume and Adequate Iodine Nutrition in Chinese Schoolchildren: Local Normative Reference Values Compared with WHO/IGN

    Directory of Open Access Journals (Sweden)

    Zhe Mo

    2016-01-01

    Full Text Available Objective. Thyroid volume measured by ultrasound to define goiter needs reliable local thyroid volume reference from iodine-sufficient populations. The aim of this study is to explore the reference interval for normal thyroid volume in schoolchildren aged 8–10 years from Zhejiang Province, China. Methods. A probability-proportionate-to-size sampling method was applied to select a representative sample of 1213 children aged 8–10 years in Zhejiang Province to detect the thyroid volume, salt iodine, and urine iodine. Results. Median urinary iodine concentration in involved schoolchildren was 178.30 (125.00 μg l−1, with the percentage of samples less than 100 μg l−1 as 12.69% and more than 300 μg l−1 as 15.25%. Thyroid volume was significantly correlated with age and anthropometric measurements independently of each other. The 97th percentile of thyroid volume in our study was larger generally than the new international reference. Conclusions. The iodine nutritional status in Zhejiang Province was at an adequate level. Despite some limitations in this study, we initially established the reference values for thyroid volume in 8–10-year-old schoolchildren in Zhejiang Province, China, as a local reference to be used for monitoring iodine deficiency disorders.

  2. Adequate trust avails, mistaken trust matters: on the moral responsibility of doctors as proxies for patients' trust in biobank research.

    Science.gov (United States)

    Johnsson, Linus; Helgesson, Gert; Hansson, Mats G; Eriksson, Stefan

    2013-11-01

    In Sweden, most patients are recruited into biobank research by non-researcher doctors. Patients' trust in doctors may therefore be important to their willingness to participate. We suggest a model of trust that makes sense of such transitions of trust between domains and distinguishes adequate trust from mistaken trust. The unique position of doctors implies, we argue, a Kantian imperfect duty to compensate for patients' mistaken trust. There are at least three kinds of mistaken trust, each of which requires a different set of countermeasures. First, trust is mistaken when necessary competence is lacking; the competence must be developed or the illusion dispelled. Second, trust is irrational whenever the patient is mistaken about his actual reasons for trusting. Care must therefore be taken to support the patient's reasoning and moral agency. Third, some patients inappropriately trust doctors to recommend only research that will benefit them directly. Such trust should be counteracted by nurturing a culture where patients expect to be asked occasionally to contribute to the common good.

  3. TNFR2 maintains adequate IL-12 production by dendritic cells in inflammatory responses by regulating endogenous TNF levels.

    Science.gov (United States)

    Martin, Elisabeth M; Remke, Annika; Pfeifer, Eva; Polz, Johannes; Pietryga-Krieger, Anne; Steffens-Weber, Dorothea; Freudenberg, Marina A; Mostböck, Sven; Männel, Daniela N

    2014-10-01

    Sepsis-induced immune reactions are reduced in TNF receptor 2 (TNFR2)-deficient mice as previously shown. In order to elucidate the underlying mechanisms, the functional integrity of myeloid cells of TNFR2-deficient mice was analyzed and compared to wild type (WT) mice. The capacity of dendritic cells to produce IL-12 was strongly impaired in TNF-deficient mice, mirroring impaired production of IL-12 by WT dendritic cells in sepsis or after LPS or TNF pre-treatment. In addition, TNFR2-deficient mice were refractory to LPS pre-treatment and also to hyper-sensitization by inactivated Propionibacterium acnes, indicating habituation to inflammatory stimuli by the immune response when TNFR2 is lacking. Constitutive expression of TNF mRNA in kidney, liver, spleen, colon and lung tissue, and the presence of soluble TNFR2 in urine of healthy WT mice supported the conclusion that TNF is continuously present in naïve mice and controlled by soluble TNFR2. In TNFR2-deficient mice endogenous TNF levels cannot be balanced and the continuous exposure to enhanced TNF levels impairs dendritic cell function. In conclusion, TNF pre-exposure suppresses secondary inflammatory reactions of myeloid cells; therefore, continuous control of endogenous TNF by soluble TNFR2 seems to be essential for the maintenance of adequate sensitivity to inflammatory stimuli.

  4. Detailed NMR, Including 1,1-ADEQUATE, and Anticancer Studies of Compounds from the Echinoderm Colobometra perspinosa

    Directory of Open Access Journals (Sweden)

    Catherine H. Liptrot

    2009-11-01

    Full Text Available From the dichloromethane/methanol extract of the crinoid Colobometra perspinosa, collected south east of Richards Island (Bedara, Family Islands, Central Great Barrier Reef, Australia, 3-(1'-hydroxypropyl-1,6,8-trihydroxy-9,10-anthraquinone [one of the two stereoisomers of rhodoptilometrin, (1], 3-propyl-1,6,8-trihydroxy-9,10-anthraquinone (3, 2-[(phenylacetylamino]ethanesulfonic acid (4, and 4-hydroxybutanoic acid (5 were isolated. Comparison of 1H- and 13C-NMR data for rhodoptilometrin (1 with those reported in the literature showed significant differences for some resonances associated with rings A and C. In an attempt to provide accurately assigned 1H- and 13C-NMR data, as well as to confirm the structure of 1, a thorough NMR investigation of this compound was undertaken. Measurements included: concentration dependent 13C, 1D selective NOE, HSQC, HMBC and 1,1-ADEQUATE. The NMR data for 4 and 5 are reported here for the first time, as is their occurrence from the marine environment. The in vitro anticancer activity of the original extract was found to be associated with 1, 3 and 5.

  5. Adequate ovarian follicular status does not prevent the decrease in pregnancy rates associated with high sperm DNA fragmentation.

    Science.gov (United States)

    Frydman, Nelly; Prisant, Nadia; Hesters, Laetitia; Frydman, René; Tachdjian, Gérard; Cohen-Bacrie, Paul; Fanchin, Rénato

    2008-01-01

    Potential reparation of sperm DNA fragmentation in the oocyte may disturb any relationship between DNA-damaged sperm and the implantation ability of resulting embryos. To rule out this factor, we analyzed the consequences of sperm DNA fragmentation on IVF-ET outcome in women with healthy ovarian function. Prospective study. Teaching hospital, France. All 117 women were <38 years old, who combined normal serum day-3 FSH and inhibin B levels with an adequate response to controlled ovarian hyperstimulation. The DNA fragmentation rate was determined in the raw sperm used for conventional IVF by flow cytometric terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay. Cycles were sorted into two groups according to whether DNA fragmentation exceeded (high fragmentation [HF], n = 52) or did not exceed (low fragmentation [LF], n = 65) the 50th percentile of values (35%). D2 embryo quality and implantation and ongoing pregnancy rates. Patients' characteristics, raw semen parameters, fertilization rates, and embryology data were similar in HF and LF groups. Clinical (37.5% vs. 62.5%) and ongoing (23.5% vs. 57.8%) pregnancy rates per ET and implantation rates (24.5% vs. 42.4%) were lower in the HF group than in the LF group. High sperm DNA fragmentation spares fertilization and top embryo morphology rates but is associated with decreased IVF-ET outcome.

  6. Presymptomatic diagnosis with MRI and adequate treatment ameliorate the outcome after natalizumab-associated progressive multifocal leukoencephalopathy (PML.

    Directory of Open Access Journals (Sweden)

    Hans eLindå

    2013-02-01

    Full Text Available Natalizumab (Tysabri® is a monoclonal antibody that prevents inflammatory cells from binding to brain endothelial cells and passing into the brain parenchyma. Natalizumab is a highly effective treatment for relapsing-remitting multiple sclerosis (MS. Progressive multifocal leukoencephalopathy (PML is an opportunistic brain JC virus infection that has been shown to be associated with natalizumab treatment. We describe PML in a patient with MS after 44 monthly infusions of natalizumab. With the aid of a routine MRI scan, PML was detected before any unambiguous clinical manifestations had emerged. PML was treated with plasma exchange to accelerate removal of natalizumab. Mirtazapine and mefloquine was promptly added and approximately one month after plasma exchange, when an immune-reconstitution-inflammatory-syndrome (IRIS appeared, steroid treatment was initiated. Steroid treatment was then continued until no virus could be detected in the cerebrospinal fluid. The outcome was favourable. We believe that this case clearly illustrates the importance of an early, presymptomatic, detection of PML and an adequate treatment. We also propose that surveillance with MRI scans, every 3 months after 24 months of treatment, should be performed in JC virus antibody positive natalizumab-treated MS patients in order to detect PML in an early phase.

  7. Are breast biopsies adequately funded? A process cost and revenue analysis; Ist die Mammabiopsie ausreichend finanziert? Eine Prozesskosten und Erloesbetrachtung

    Energy Technology Data Exchange (ETDEWEB)

    Hahn, M.; Fischbach, E.; Fehm, T. [Universitaetsklinikum Tuebingen (DE). Dept. of Obstetrics and Gynecology] (and others)

    2011-04-15

    Purpose: The objective of the study was to determine whether the various breast biopsy procedures specified in the S 3 guidelines are sensibly represented within the current German health system as considered from a cost evaluation perspective. Materials and Methods: This prospectively designed multicenter study analyzed 221 breast biopsies at 7 institutions from 04/2006 to 01/2007. Core needle biopsies, vacuum-assisted biopsies and surgical open biopsies under sonographic or mammographic guidance were evaluated. During an analysis of process costs, the individual process steps were recorded in diagrammatic form and assigned to the true consumption of resources. The actual resource consumption costs were entered. A process-related breakeven analysis was conducted to check whether the reimbursement of individual biopsy types covers the costs. Results: Only sonographically guided core needle biopsy and surgical open biopsy are adequately reimbursed in the current German health system. All other breast biopsies indicate a negative profit margin. The principal reasons for underfunding are found in the area of reimbursement of investment and non-personnel costs. Conclusion: The reimbursement of breast biopsies must be improved in order to guarantee nationwide care of the population using the breast biopsy methods recommended in the S 3 guidelines and to avoid disincentives with respect to breast biopsy indications. (orig.)

  8. Small noncoding RNAs in cells transformed by human T-cell leukemia virus type 1: a role for a tRNA fragment as a primer for reverse transcriptase.

    Science.gov (United States)

    Ruggero, Katia; Guffanti, Alessandro; Corradin, Alberto; Sharma, Varun Kumar; De Bellis, Gianluca; Corti, Giorgio; Grassi, Angela; Zanovello, Paola; Bronte, Vincenzo; Ciminale, Vincenzo; D'Agostino, Donna M

    2014-04-01

    The present study employed mass sequencing of small RNA libraries to identify the repertoire of small noncoding RNAs expressed in normal CD4(+) T cells compared to cells transformed with human T-cell leukemia virus type 1 (HTLV-1), the causative agent of adult T-cell leukemia/lymphoma (ATLL). The results revealed distinct patterns of microRNA expression in HTLV-1-infected CD4(+) T-cell lines with respect to their normal counterparts. In addition, a search for virus-encoded microRNAs yielded 2 sequences that originated from the plus strand of the HTLV-1 genome. Several sequences derived from tRNAs were expressed at substantial levels in both uninfected and infected cells. One of the most abundant tRNA fragments (tRF-3019) was derived from the 3' end of tRNA-proline. tRF-3019 exhibited perfect sequence complementarity to the primer binding site of HTLV-1. The results of an in vitro reverse transcriptase assay verified that tRF-3019 was capable of priming HTLV-1 reverse transcriptase. Both tRNA-proline and tRF-3019 were detected in virus particles isolated from HTLV-1-infected cells. These findings suggest that tRF-3019 may play an important role in priming HTLV-1 reverse transcription and could thus represent a novel target to control HTLV-1 infection. Small noncoding RNAs, a growing family of regulatory RNAs that includes microRNAs and tRNA fragments, have recently emerged as key players in many biological processes, including viral infection and cancer. In the present study, we employed mass sequencing to identify the repertoire of small noncoding RNAs in normal T cells compared to T cells transformed with human T-cell leukemia virus type 1 (HTLV-1), a retrovirus that causes adult T-cell leukemia/lymphoma. The results revealed a distinct pattern of microRNA expression in HTLV-1-infected cells and a tRNA fragment (tRF-3019) that was packaged into virions and capable of priming HTLV-1 reverse transcription, a key event in the retroviral life cycle. These findings

  9. Personal attributes that influence the adequate management of hypertension and dyslipidemia in patients with type 2 diabetes. Results from the DIAB-CORE Cooperation

    National Research Council Canada - National Science Library

    Rückert, Ina-Maria; Maier, Werner; Mielck, Andreas; Schipf, Sabine; Völzke, Henry; Kluttig, Alexander; Greiser, Karin-Halina; Berger, Klaus; Müller, Grit; Ellert, Ute; Neuhauser, Hannelore; Rathmann, Wolfgang; Tamayo, Teresa; Moebus, Susanne; Andrich, Silke; Meisinger, Christa

    2012-01-01

    .... In the current study we evaluated individual characteristics that are assumed to influence the adequate treatment and control of hypertension and dyslipidemia and aimed to identify the patient group...

  10. STUDIES REGARDING THE DETERMINATION OF THE ADEQUATE ASSEMBLY TOLERANCES DEPENDING ON THE MANUFACTURING COSTS OF THE PARTS PROCESSED ON CLASSIC MACHINE TOOLS

    Directory of Open Access Journals (Sweden)

    Constanţa RĂDULESCU

    2010-06-01

    Full Text Available The paper deals with a study case regarding the determination of adequate assembly tolerances. The study concerned the assembly of two bearings on an axle. Determining the adequate tolerances of the sizes chains is based on Lagrange’s multipliers use. The optimization criterion for determining the assembly tolerances is the minimization of the product achievement cost. The relation between tolerances and cost will be revealed in a graphic component

  11. Conservation of RNA sequence and cross-linking ability in ribosomes from a higher eukaryote: photochemical cross-linking of the anticodon of P site bound tRNA to the penultimate cytidine of the UACACACG sequence in Artemia salina 18S rRNA.

    Science.gov (United States)

    Ciesiolka, J; Nurse, K; Klein, J; Ofengand, J

    1985-06-18

    The complex of Artemia salina ribosomes and Escherichia coli acetylvalyl-tRNA could be cross-linked by irradiation with near-UV light. Cross-linking required the presence of the codon GUU, GUA being ineffective. The acetylvalyl group could be released from the cross-linked tRNA by treatment with puromycin, demonstrating that cross-linking had occurred at the P site. This was true both for pGUU- and also for poly(U2,G)-dependent cross-linking. All of the cross-linking was to the 18S rRNA of the small ribosomal subunit. Photolysis of the cross-link at 254 nm occurred with the same kinetics as that for the known cyclobutane dimer between this tRNA and Escherichia coli 16S rRNA. T1 RNase digestion of the cross-linked tRNA yielded an oligonucleotide larger in molecular weight than any from un-cross-linked rRNA or tRNA or from a prephotolyzed complex. Extended electrophoresis showed this material to consist of two oligomers of similar mobility, a faster one-third component and a slower two-thirds component. Each oligomer yielded two components on 254-nm photolysis. The slower band from each was the tRNA T1 oligomer CACCUCCCUVACAAGp, which includes the anticodon. The faster band was the rRNA 9-mer UACACACCGp and its derivative UACACACUG. Unexpectedly, the dephosphorylated and slower moving 9-mer was derived from the faster moving dimer. Deamination of the penultimate C to U is probably due to cyclobutane dimer formation and was evidence for that nucleotide being the site of cross-linking. Direct confirmation of the cross-linking site was obtained by "Z"-gel analysis [Ehresmann, C., & Ofengand, J. (1984) Biochemistry 23, 438-445].(ABSTRACT TRUNCATED AT 250 WORDS)

  12. High prevalence of maternal hypothyroidism despite adequate iodine status in Indian pregnant women in the first trimester.

    Science.gov (United States)

    Jaiswal, Nidhi; Melse-Boonstra, Alida; Thomas, Tinku; Basavaraj, Chetana; Sharma, Surjeet Kaur; Srinivasan, Krishnamachari; Zimmermann, Michael B

    2014-09-01

    Iodine requirements are increased during pregnancy to maintain maternal and fetal euthyroidism. There have been recent improvements in iodized salt coverage in India, but whether iodized salt is sufficient to sustain iodine requirements during pregnancy remains uncertain. Our aims were to measure thyroid status in first trimester pregnant women in southern India and assess potential determinants of thyroid function, including iodine status, thyroid autoimmunity, dietary patterns, body weight, and anemia. This was a cross-sectional study among 334 pregnant women of ≤ 14 weeks' gestation, in Bangalore, India. We measured anthropometrics, urinary iodine concentration (UIC), maternal thyroid volume (by ultrasound), and thyroid function. We applied a thyrotropin (TSH) upper limit of 2.5 mIU/L to classify thyroid insufficiency. Using a questionnaire, we obtained sociodemographic and dietary data, obstetric history, and use of iodized salt and iodine supplements. Among the women, the mean (standard deviation) gestational age was 10.3 (2.5) weeks, 67% were nulliparous, 21% were vegetarian, 19% were anemic, and 23% were overweight or obese. Iodized salt was used by 98% of women, and they were iodine sufficient: median UIC (range) was 184.2 μg/L (8.1-1152 μg/L) and all had a normal thyroid volume. However, 18% of the women had thyroid insufficiency: 3.7% had overt hypothyroidism (83% with positive TPO-Ab), 9.2% had subclinical hypothyroidism, and 5.2% had hypothyroxinemia. Women consuming vegetarian diets did not have significantly lower iodine intakes or higher risk of hypothyroidism than those consuming mixed diets, but overweight/obesity and anemia predicted thyroid insufficiency. In this urban population of southern India, pregnant women have adequate iodine status in the first trimester. Despite this, many have thyroid insufficiency, and the prevalence of overt hypothyroidism is more than fivefold higher than reported in other iodine sufficient populations of

  13. The feasibility of producing adequate feedstock for year–round cellulosic ethanol production in an intensive agricultural fuelshed

    Science.gov (United States)

    Uden, Daniel R.; Mitchell, Rob B.; Allen, Craig R.; Guan, Qingfeng; McCoy, Tim D.

    2013-01-01

    To date, cellulosic ethanol production has not been commercialized in the United States. However, government mandates aimed at increasing second-generation biofuel production could spur exploratory development in the cellulosic ethanol industry. We conducted an in-depth analysis of the fuelshed surrounding a starch-based ethanol plant near York, Nebraska that has the potential for cellulosic ethanol production. To assess the feasibility of supplying adequate biomass for year-round cellulosic ethanol production from residual maize (Zea mays) stover and bioenergy switchgrass (Panicum virgatum) within a 40-km road network service area of the existing ethanol plant, we identified ∼14,000 ha of marginally productive cropland within the service area suitable for conversion from annual rowcrops to switchgrass and ∼132,000 ha of maize-enrolled cropland from which maize stover could be collected. Annual maize stover and switchgrass biomass supplies within the 40-km service area could range between 429,000 and 752,000 metric tons (mT). Approximately 140–250 million liters (l) of cellulosic ethanol could be produced, rivaling the current 208 million l annual starch-based ethanol production capacity of the plant. We conclude that sufficient quantities of biomass could be produced from maize stover and switchgrass near the plant to support year-round cellulosic ethanol production at current feedstock yields, sustainable removal rates and bioconversion efficiencies. Modifying existing starch-based ethanol plants in intensive agricultural fuelsheds could increase ethanol output, return marginally productive cropland to perennial vegetation, and remove maize stover from productive cropland to meet feedstock demand.

  14. Expression Profile of Genes Potentially Associated with Adequate Glycemic Control in Patients with Type 2 Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Sâmia Cruz Tfaile Corbi

    2017-01-01

    Full Text Available Despite increasing research in type 2 diabetes mellitus (T2D, there are few studies showing the impact of the poor glycemic control on biological processes occurring in T2D. In order to identify potential genes related to poorly/well-controlled patients with T2D, our strategy of investigation included a primary screen by microarray (Human Genome U133 in a small group of individuals followed by an independent validation in a greater group using RT-qPCR. Ninety patients were divided as follows: poorly controlled T2D (G1, well-controlled T2D (G2, and normoglycemic individuals (G3. After using affy package in R, differentially expressed genes (DEGs were prospected as candidate genes potentially relevant for the glycemic control in T2D patients. After validation by RT-qPCR, the obtained DEGs were as follows—G1 + G2 versus G3: HLA-DQA1, SOS1, and BRCA2; G2 versus G1: ENO2, VAMP2, CCND3, CEBPD, LGALS12, AGBL5, MAP2K5, and PPAP2B; G2 versus G3: HLA-DQB1, MCM4, and SEC13; and G1 versus G3: PPIC. This demonstrated a systemic exacerbation of the gene expression related to immune response in T2D patients. Moreover, genes related to lipid metabolisms and DNA replication/repair were influenced by the glycemic control. In conclusion, this study pointed out candidate genes potentially associated with adequate glycemic control in T2D patients, contributing to the knowledge of how the glycemic control could systemically influence gene expression.

  15. Mutation Analysis of Mitochondrial tRNA Gene in Patients with Primary Dilated Cardiomyopathy%原发性扩张型心肌病的线粒体tRNA基因突变分析

    Institute of Scientific and Technical Information of China (English)

    李红超; 舒红英; 李晓杰; 倪斌; 谢海龙; 周海燕; 倪崖

    2015-01-01

    To identify the potential pathogenic mutations of mitochondrial tRNA in patients with primary dilated cardio-myopathy(DCM) and the possible association of the mutations with DCM.Paraffin-embedded myocardial tissues from two patients with DCM and 10 healthy controls,which were discarded after forensic examination,were used for the study.PCR amplification wasperformed for the mitochondrial tRNA genes and direct sequencing was conducted.Sequencing re-sults showed no variation for mitochondrial tRNA genes in the normal myocardial tissues.The tRNAVal G1664A variation and tRNAMet T4454C variation were identified in patients with DCM.These two variations were previously reported as polymorphism in MitoMap.There was no pathogenic mutation detected in mitochondrial tRNA genes of the two patients with DCM.A patient pool of large sample size is expected for analysis of the pathogenic mutations,polymorphism loci and haplogroup that might be associated with DCM.%为寻找原发性扩张型心肌病病例是否存在已知以及未知的线粒体tRNA致病性突变,以探讨扩张型心肌病可能的发病原因.收集2例原发性扩张型心肌病患者和10例正常对照尸检心肌组织石蜡标本,针对22种线粒体tRNA基因分别设计一对引物,PCR扩增后并测序分析线粒体tRNA基因突变情况.结果在对照样本中未检测到线粒体tRNA变异位点,在1例患者中检测到了tRNAVal基因G1664A变异,Mitomap已有报道为多态性位点;于另1例患者中检测到tRNAMetT4454C变异,有文章报道该位点与线粒体功能障碍有关,Mitomap报道为多态性位点.本研究中2例病例中未检测到线粒体tRNA致病性突变位点,可能与病例个体的心衰程度有关,有必要扩大样本量深入研究线粒体tRNA以及mtDNA其他基因突变与原发性扩张型心肌病之间的关系,以寻找可能的致病突变位点、易感的多态性位点或者单倍体群,为认识原发性扩张型心肌病的发病机制进一步提供理论基础和依据.

  16. An 18.3 kb DNA fragment from yeast chromosome VII carries four unknown open reading frames, the gene for an Asn synthase, remnants of Ty and three tRNA genes.

    Science.gov (United States)

    Van Dyck, L; Tettelin, H; Purnelle, B; Goffeau, A

    1997-02-01

    An 18.3 kb DNA segment from yeast Saccharomyces cerevisiae VII encompasses the previously characterized MEP1, NUP57 and PPT1 genes as well as seven new open reading frames (ORFs) of at least 100 residues. G6358 is an ubiquitous glutamine-dependent asparagine synthase. G6362 is membrane protein highly homologous to a protein of unknown function in the yeast Schizosaccharomyces pombe. Three ORFs (G6324, G6335 and G6365) have no significant homology with previously reported proteins of characteristic motifs. G6321 and G6359, enclosed in longer ORFs, are not likely to be coding. The segment also contains tRNA genes for Asn, Arg and Ile as well as sigma element and two solo deltas. ORFs and genetic elements are named according to a preliminary working nomenclature.

  17. 硒代半胱氨酸合成蛋白基因表达对过氧化氢介导的内皮细胞EVC-304损伤的影响%Relationship between expression of selenocysteine synthase and endothelial cell line ECV-304 injury induced by hydrogen peroxide

    Institute of Scientific and Technical Information of China (English)

    赵汉东; 孙美娜; 李凤兰; 李晖

    2014-01-01

    Objective To observe the influence of selenocysteine synthase(SEPSECS) on injury of human umbilical vein endothelial cell line EVC-304 induced by hydrogen peroxide (H2O2). Methods Transfection was conducted to transfect EVC-304 which was maintained in vitro. The cells were divided into four groups: control group, SEPSECS over-expression group, empty vector group and SEPSECS silenced expression group, then Real-time PCR and Western blotting were performed to detected SEPSECS mRNA and protein expression , respectively. Flow cytometry(FCM) was performed to detect cell cycle. Different concentrations of H2O2, which including 0, 200, 400, 600, 800, 1 000 μmol/L, were used to treat EVC-304 . Then malonaldehyde (MDA), superoxide dismutase(SOD) secreted by the cells which were treated with H2O2 for 6 h, were checked by MDA or SOD kit. Results The SEPSECS mRNA expressions of control, SEPSECS silenced expression, empty vector and SEPSECS over-expression groups were 1.03 ± 0.24, 0.43 ± 0.11, 0.98 ± 0.27 and 1.61 ± 0.13, respectively. The protein expressions of control, SEPSECS silenced expression, empty vector and SEPSECS over-expression groups were 1.00 ± 0.26, 0.51 ± 0.10, 1.12 ± 0.38 and 1.51 ± 0.20, respectively. There was a significant difference between control and SEPSECS silenced expression groups (all P 0.05). Meanwhile, MDA of SEPSECS silenced expression groups[(15.8 ± 0.5),(19.6 ± 1.5)μmol/L] were significantly higher than control groups[(12.4 ± 0.1),(17.1 ± 0.5)μmol/L, all P 0.05)。经H2O2处理的各组EVC-304细胞MDA含量均随H2O2浓度的升高而升高。其中H2O2为800、1000μmol/L时,SEPSECS低表达组MDA含量[(15.8±0.5)、(19.6±1.5)μmol/L]明显高于对照组[(12.4±0.1)、(17.1±0.5)μmol/L,P均<0.05],SEPSECS高表达组MDA含量[(10.8±0.4)、(14.2±1.1)μmol/L]明显低于空载体转染组[(12.7±0.7)、(16.2±1.1)μmol/L,P均<0.05]。经H2O2处理的各组EVC-304

  18. Escherichia coli methionyl-tRNA formyltransferase: role of amino acids conserved in the linker region and in the C-terminal domain on the specific recognition of the initiator tRNA.

    Science.gov (United States)

    Gite, S; Li, Y; Ramesh, V; RajBhandary, U L

    2000-03-01

    The formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for the initiation of protein synthesis in eubacteria. We are studying the molecular mechanisms of recognition of the initiator tRNA by Escherichia coli MTF. MTF from eubacteria contains an approximately 100-amino acid C-terminal extension that is not found in the E. coli glycinamide ribonucleotide formyltransferase, which, like MTF, use N(10)-formyltetrahydrofolate as a formyl group donor. This C-terminal extension, which forms a distinct structural domain, is attached to the N-terminal domain through a linker region. Here, we describe the effect of (i) substitution mutations on some nineteen basic, aromatic and other conserved amino acids in the linker region and in the C-terminal domain of MTF and (ii) deletion mutations from the C-terminus on enzyme activity. We show that the positive charge on two of the lysine residues in the linker region leading to the C-terminal domain are important for enzyme activity. Mutation of some of the basic amino acids in the C-terminal domain to alanine has mostly small effects on the kinetic parameters, whereas mutation to glutamic acid has large effects. However, the deletion of 18, 20, or 80 amino acids from the C-terminus has very large effects on enzyme activity. Overall, our results support the notion that the basic amino acid residues in the C-terminal domain provide a positively charged channel that is used for the nonspecific binding of tRNA, whereas some of the amino acids in the linker region play an important role in activity of MTF.

  19. AnnAGNPS model as a potential tool for seeking adequate agriculture land management in Navarre (Spain)

    Science.gov (United States)

    Chahor, Y.; Giménez, R.; Casalí, J.

    2012-04-01

    runoff was. On the other hand, a significant increment (30%) on annual sediment yield was predicted when rapeseed is the alternative major crop. Besides, a large decrease in annual runoff (up to 41%) and sediment (up to 98%) was predicted as the watershed is gradually occupied by shrubs. Finally, no-tillage appears as an interesting management method for cereals, with an over 90% reduction of in sediment yield -but only 4% in runoff. This is a first approach to evaluate AnnAGNPS as a management tool under local conditions. The above results may be then taking with caution especially in terms of absolute predicted values. However, AnnAGNPS can be considered as a promising tool for assessing the effect of the agricultural activities and implementing adequate land management alternatives in Mediterranean environment.

  20. Differences in whole-body protein turnover between Iberian and Landrace pigs fed adequate or lysine-deficient diets.

    Science.gov (United States)

    Rivera-Ferre, M G; Aguilera, J F; Nieto, R

    2006-12-01

    The capacity for protein deposition in Iberian pigs is lower than in modern (e.g., Landrace) pig breeds, and the reasons for this remain unknown. The hypothesis tested in this work is that under similar nutritional and physiological conditions, whole-body protein turnover as well as the protein synthesis to protein deposition ratio differs between Iberian and Landrace breeds, resulting in dissimilar protein deposition rates. As a main objective, these variables were compared at different protein and Lys intakes in growing gilts. The study examined the effect of Lys deficiency because this is the prevalent condition during the fattening period of the Iberian pig in the Mediterranean forest, where the main feed source is oak acorn, which provides approximately one-third of the available Lys present in an ideal protein. Three diets were tested within each breed: 2 diets with an optimal essential AA pattern, containing 12 or 16% CP as-fed, or a Lys-deficient diet (35% of the recommended Lys content). This diet was supplied at 12% CP for the Iberian and 16% CP for the Landrace pigs, respectively. The contrasts made were breed x dietary protein concentration and breed x AA pattern (adequate vs. inadequate Lys content). Cumulative urinary (15)N excretion over 60 h after receiving an oral dose of [(15)N]-glycine was used to calculate N flux. Mean BW for Landrace and Iberian pigs were 25.8 +/- 0.55 kg and 30.8 +/- 0.74 kg, respectively. Protein deposition (g of N/(kg(0.75).d) was lower in the Iberian than in the Landrace gilts (4 to 16%; P = 0.002) and increased with dietary protein content. In contrast, protein synthesis and degradation [g of N/(kg(0.75).d)] were greater for the Landrace breed (16 to 18 and 23%, respectively, for the 2 dietary protein contents studied; P Landrace pigs than in Iberian pigs fed optimal AA-pattern diets were then attributed to differences in body protein mass. Consequently, these results validate the hypothesis of unequal synthesis and

  1. [Medical care unit -- a suitable instrument for ambulatory patient-adequate care and performance-related remuneration].

    Science.gov (United States)

    Rudolph, P; Isensee, D; Gerlach, E; Gross, H

    2013-02-01

    The question of whether a medical care unit is an appropriate tool for outpatient care has been discussed for a long time. Our aim is to investigate whether the MCU is an effective instrument for outpatient care and adequate performance-related remuneration. This retro- and prospective overview of the work included statements on legal foundations for medical care units, for reimbursement of services in medical care units, the development of medical care centres in Germany and a listing of the specific advantages and disadvantages of an MCU. This article focuses on the generally applicable facts and complements them with examples from general, visceral and vascular surgery. The main quantitative data on medical centre statistics come from different publications of the National Association of Statutory Health Insurance for Physicians. From a legal point of view the instrument MCU allows the participating of ambulatory and stationary care in the framework of medical care contracts. This has been especially extended for stationary applications, including the spectrum of possibilities that can contribute under certain circumstances for the provision of medical care in underdeveloped regions. Freelancers can benefit primarily from financial risk and minimising bureaucratic routine. The remuneration for services performed in the MCU is analogous to that of other ambulatory care providers. Basically, there are no disadvantages, but a greater design freedom and opportunities for the generation of aggregates are visible. The number of MCU in Germany has quadrupled in the last five years, indicating an establishment of an outpatient care landscape. MCU offers from the patient's perspective, providers and policy specific advantages and disadvantages. Indeed the benefits outweigh the disadvantages, but this is not yet verified by qualitative studies. The question of the appropriateness of medical care units as outpatient care instrumentation must be considered differentially

  2. An Increase in Consuming Adequately Iodized Salt May Not Be Enough to Rectify Iodine Deficiency in Pregnancy in an Iodine-Sufficient Area of China

    Science.gov (United States)

    Wang, Zhifang; Zhu, Wenming; Mo, Zhe; Wang, Yuanyang; Mao, Guangming; Wang, Xiaofeng; Lou, Xiaoming

    2017-01-01

    Universal salt iodization (USI) has been implemented for two decades in China. It is crucial to periodically monitor iodine status in the most vulnerable population, such as pregnant women. A cross-sectional study was carried out in an evidence-proved iodine-sufficient province to evaluate iodine intake in pregnancy. According to the WHO/UNICEF/ICCIDD recommendation criteria of adequate iodine intake in pregnancy (150–249 µg/L), the median urinary iodine concentration (UIC) of the total 8159 recruited pregnant women was 147.5 µg/L, which indicated pregnant women had iodine deficiency at the province level. Overall, 51.0% of the total study participants had iodine deficiency with a UIC < 150 µg/L and only 32.9% of them had adequate iodine. Participants living in coastal areas had iodine deficiency with a median UIC of 130.1 µg/L, while those in inland areas had marginally adequate iodine intake with a median UIC of 158.1 µg/L (p < 0.001). Among the total study participants, 450 pregnant women consuming non-iodized salt had mild-moderate iodine deficiency with a median UIC of 99.6 µg/L; 7363 pregnant women consuming adequately iodized salt had a lightly statistically higher median UIC of 151.9 µg/L, compared with the recommended adequate level by the WHO/UNICEF/ICCIDD (p < 0.001). Consuming adequately iodized salt seemed to lightly increase the median UIC level, but it may not be enough to correct iodine nutrition status to an optimum level as recommended by the WHO/UNICEF/ICCIDD. We therefore suggest that, besides strengthening USI policy, additional interventive measure may be needed to improve iodine intake in pregnancy. PMID:28230748

  3. The effect of virginiamycin in diets with adequate or reduced dietary calcium or nonphytate phosphorus for broilers.

    Science.gov (United States)

    O'Connor-Dennie, T; Southern, L L

    2005-12-01

    Four experiments (EXP) were conducted to evaluate the effects of virginiamycin (Vm) in diets adequate or reduced in Ca or nonphytate P (nPP) levels on growth performance and bone response variables in chicks. All diets were corn-soybean meal (C-SBM) based, and all treatments were replicated 6 or 8 times with 5 or 6 chicks each. In EXP 1 and 2, the dietary treatments were 1) C-SBM with 1.00% Ca and 0.45% nPP (positive control; PC); 2) C-SBM with 0.80% Ca and 0.45% nPP (0.80Ca); 3) C-SBM with 1.00% Ca and 0.35% nPP (0.35nPP); and 4 to 6) Diets 1 to 3 with 11 (EXP 1) or 22 (EXP 2) ppm of Vm. In EXP 1, daily gain (ADG), feed intake (ADFI), bone breaking strength (BBS), milligrams of ash per gram of Ca intake (ASH/Ca), and BBS per gram of Ca (BBS/Ca) or nPP (BBS/nPP) intake were increased in chicks fed Vm (P < 0.04 to 0.07). Chicks fed the 0.35nPP diet with Vm had increased ADG, ADFI, BBS, milligrams of tibia ash (ASH), BBS/Ca, and BBS/nPP (nPP x Vm, P < 0.03 to 0.10). Chicks fed the 0.80Ca diet with Vm had increased ASH, milligrams of ASH per gram of nPP intake (ASH/ nPP), and ASH/Ca (P < 0.01 to 0.09). Tibia ash, BBS, gain:feed (G:F), BBS/nPP, and ASH/nPP were decreased in chicks fed the 0.80Ca diet (P < 0.01 to 0.07). Bone ash percentage (BAP), BBS, BBS/Ca, ASH, and ASH/Ca were decreased in chicks fed the 0.35nPP diets (P < 0.01); ASH/ nPP was increased (P < 0.01). In EXP 2, BAP, ASH, ASH/ Ca, and ASH/nPP were increased in chicks fed Vm (P < 0.02 to 0.07). Chicks fed the 0.80Ca diet had a decreased ASH/nPP (P < 0.04) but an increased BBS/Ca and ASH/ Ca (P < 0.01 to 0.02). Chicks fed the 0.35nPP diet had decreased ADG, ADFI, G:F, BBS, BAP, ASH, ASH/Ca, and BBS/Ca (P < 0.01 to 0.04), but BBS/nPP and ASH/ nPP were increased (P < 0.01 to 0.04). In EXP 3, the dietary treatments were 1) PC; 2) C-SBM with 0.70% Ca and 0.45% nPP (0.70Ca); 3) C-SBM with 1.00% Ca and 0.25% nPP (0.25nPP); 4 to 6) Diets 1 to 3 with 9 ppm of Vm. The addition of Vm to the 0.25nPP diet decreased

  4. Intelligence, Academic Self-Concept, and Information Literacy: The Role of Adequate Perceptions of Academic Ability in the Acquisition of Knowledge about Information Searching

    Science.gov (United States)

    Rosman, Tom; Mayer, Anne-Kathrin; Krampen, Günter

    2015-01-01

    Introduction: The present paper argues that adequate self-perceptions of academic ability are essential for students' realization of their intellectual potential, thereby fostering learning of complex skills, e.g., information-seeking skills. Thus, academic self-concept should moderate the relationship between intelligence and information…

  5. THE INFLUENCE FACTORS OF POWER AND OWNERSHIP ON THE FORMATION OF CONFIGURATIONS OF THE CAPITALS OF THE MODERN CORPORATION, ADEQUATE TO THE CHARACTERISTICS OF DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Yermolenko V. V.

    2015-12-01

    Full Text Available The article examines the influence of key factors in the development of modern corporations – the authorities and property for the effective realization of the expanded reproduction of generative type. The article reveals a problem of building an effective configuration of capital (capitalograms and an adequate system of existing development strategies of a corporation. It also formulates research hypothesis

  6. Risk factors for childhood overweight in offspring of type 1 diabetic women with adequate glycemic control during pregnancy: Nationwide follow-up study in the Netherlands

    NARCIS (Netherlands)

    M. Rijpert; I.M. Evers; M.A.M.J. de Vroede; H.W. de Valk; C.J. Heijnen; G.H.A. Visser

    2009-01-01

    OBJECTIVE - Pregnancy in type 1 diabetic women remains a high-risk situation for both mother and child. In this study, we investigated long-term effects on body composition, prevalence of overweight, and insulin resistance in children of type 1 diabetic women who had had adequate glycemic control du

  7. A Method of Construction for Abundant Semigroups with a CO-Adequate Transversal%具有CO-恰当断面富足半群的一种构造方法

    Institute of Scientific and Technical Information of China (English)

    李勇华; 何勇

    2008-01-01

    In this paper, we first study the structure of quasi-adequate semigroups with a cancellative monoid transversal. By using the above result, we present a method of construction for the abundant semigroups containing a CO-adequate transversal.

  8. Correction of the consequences of mitochondrial 3243A>G mutation in the MT-TL1 gene causing the MELAS syndrome by tRNA import into mitochondria.

    Science.gov (United States)

    Karicheva, Olga Z; Kolesnikova, Olga A; Schirtz, Tom; Vysokikh, Mikhail Y; Mager-Heckel, Anne-Marie; Lombès, Anne; Boucheham, Abdeldjalil; Krasheninnikov, Igor A; Martin, Robert P; Entelis, Nina; Tarassov, Ivan

    2011-10-01

    Mutations in human mitochondrial DNA are often associated with incurable human neuromuscular diseases. Among these mutations, an important number have been identified in tRNA genes, including 29 in the gene MT-TL1 coding for the tRNA(Leu(UUR)). The m.3243A>G mutation was described as the major cause of the MELAS syndrome (mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes). This mutation was reported to reduce tRNA(Leu(UUR)) aminoacylation and modification of its anti-codon wobble position, which results in a defective mitochondrial protein synthesis and reduced activities of respiratory chain complexes. In the present study, we have tested whether the mitochondrial targeting of recombinant tRNAs bearing the identity elements for human mitochondrial leucyl-tRNA synthetase can rescue the phenotype caused by MELAS mutation in human transmitochondrial cybrid cells. We demonstrate that nuclear expression and mitochondrial targeting of specifically designed transgenic tRNAs results in an improvement of mitochondrial translation, increased levels of mitochondrial DNA-encoded respiratory complexes subunits, and significant rescue of respiration. These findings prove the possibility to direct tRNAs with changed aminoacylation specificities into mitochondria, thus extending the potential therapeutic strategy of allotopic expression to address mitochondrial disorders.

  9. DO FINANCIAL STATEMENTS PROVIDE ADEQUATE INFORMATION ABOUT THE CAPITALIZATION OF COSTS RELATED TO INTANGIBLE ASSETS?: AN EMPIRICAL RESEARCH ON ITALIAN LISTED COMPANIES

    OpenAIRE

    Vignini, Stefania

    2015-01-01

    The aim of our research is to verify if Italian listed companies financial statements provide adequate information about the capitalization of costs related to intangible assets and if the information provided are reliable. Moreover, we investigated if they merely comply with law or provide additional information on cost capitalization and reveal if internal control systems (especially managerial accounting systems) or other information systems are applied to support the measurement proces...

  10. Frequency of the adequate use of statistical tests of hypothesis in original articles published in the Revista Brasileira de Anestesiologia between January 2008 and December 2009.

    Science.gov (United States)

    Barbosa, Fabiano Timbó; de Souza, Diego Agra

    2010-01-01

    Statistical analysis is necessary for adequate evaluation of the original article by the reader allowing him/her to better visualize and comprehend the results. The objective of the present study was to determine the frequency of the adequate use of statistical tests in original articles published in the Revista Brasileira de Anestesiologia from January 2008 to December 2009. Original articles published in the Revista Brasileira de Anestesiologia between January 2008 and December 2009 were selected. The use of statistical tests was deemed appropriate when the selection of the tests was adequate for continuous and categorical variables and for parametric and non-parametric tests, the correction factor was described when the use of multiple comparisons was reported, and the specific use of a statistical test for analysis of one variable was mentioned. Seventy-six original articles from a total of 179 statistical tests were selected. The frequency of the statistical tests used more often was: Chi-square 20.11%, Student t test 19.55%, ANOVA 10.05%, and Fisher exact test 9.49%. The frequency of the adequate use of statistical tests was 56.42% (95% CI 49.16% to 63.68%), erroneous use in 13.41% (95% CI 8.42% to 18.40%), and an inconclusive result in 30.16% (95% CI 23.44% to 36.88%). The frequency of inadequate use of statistical tests in the articles published by the Revista Brasileira de Anestesiologia between January 2008 and December 2009 was 56.42%. Copyright © 2010 Elsevier Editora Ltda. All rights reserved.

  11. Multiple giant succular and fusiform right and left coronary artery aneurysms after early and adequate treatment of atypical kawasaki disease with unusual presentation.

    Directory of Open Access Journals (Sweden)

    Mostafa Behjati-Ardakani

    2014-06-01

    Full Text Available The major complication of Kawasaki disease is coronary artery dilatation and aneurysm. It occurs in approximately 15-25% of untreated children with Kawasaki Disease. Early diagnosis and treatment with Intravenous immune globulin (IVIG and aspirin (ASA can reduce the incidence of coronary artery abnormality to 2%-5%. We report one case of Atypical Kawasaki Disease with Multiple giant coronary artery aneurysms despite early adequate treatment with IVIG and ASA.

  12. Abrupt laryngeal engagement during stop plosive-vowel transitions in children with repaired cleft palate and adequate velopharyngeal closure: aerodynamic and sound pressure level evidence.

    Science.gov (United States)

    Zajac, David J; Milholland, Sarah

    2014-01-01

    To determine whether children with repaired cleft palate and adequate velopharyngeal closure exhibit abrupt laryngeal engagement during stop plosive-vowel transitions as compared with children without cleft palate. A prospective group design was used with convenience sampling of patients at a university craniofacial center. PARTICIPANTS were 25 children (15 boys, 10 girls) with repaired cleft palate (mean age = 10.9 years, standard deviation = 1.5 years) and 20 children (10 boys, 10 girls) without cleft palate (mean age = 10.8 years, standard deviation = 1.8 years). All children with cleft palate had adequate velopharyngeal closure as determined by aerodynamic testing. (1) Peak oral airflow was determined during the release of /t/ in the word "two" during a counting task. (2) An index of laryngeal engagement defined as the ratio of the maximum oral airflow declination to peak oral airflow was calculated during the release of /t/. (3) Sound pressure level was determined during the vowel of the word "two." Children with cleft palate exhibited significantly more negative laryngeal engagement ratios (i.e., more abrupt adduction) (P = .002) and greater sound pressure level (P = .049) than controls. There was a significant negative relationship between laryngeal engagement and sound pressure level for all children (r = -.428, P = .003). Children with repaired cleft palate and adequate velopharyngeal function appear to use a strategy of abrupt laryngeal adduction during stop plosive-vowel transitions. This strategy-perhaps learned even prior to palate surgery-may help to achieve either adequate sound pressure level and/or velopharyngeal closure.

  13. Adequate prenatal care reduces the risk of adverse pregnancy outcomes in women with history of infertility: a nationwide population-based study.

    Science.gov (United States)

    Alibekova, Raushan; Huang, Jian-Pei; Chen, Yi-Hua

    2013-01-01

    To investigate the effects of various measures of prenatal care on adverse pregnancy outcomes in women with a history of infertility. A retrospective cohort study. Data were derived by linking 2 large nationwide population-based datasets, the National Health Insurance Research Database and Taiwan Birth Certificate Registry. The study sample included 15,056 women with an infertility diagnosis and 60,224 randomly selected women without infertility matched to the study sample by maternal age. A conditional logistic regression analysis was performed for the analysis. Women diagnosed with infertility respectively had 1.39 (95% CI, 1.06~1.83), 1.15 (95% CI, 1.08~1.24), 1.13 (95% CI, 1.08~1.18), and 1.08 (95% CI, 1.05~1.12) higher odds of having very low birth weight (VLBW) babies, preterm births, labor complications, and cesarean sections (CSs) compared to women without infertility. Inadequate numbers of total and major prenatal visits and late initiation of prenatal care increased the risks of adverse pregnancy outcomes in women with infertility, especially the risk of a VLBW baby. However, no significant associations were found for the risks of adverse birth outcomes in infertile women with adequate prenatal care compared to fertile women with adequate care. Study findings suggest that adequate prenatal care can reduce the risk of adverse pregnancy outcomes in women with infertility.

  14. Perceptions on the right to adequate food after a major landslide disaster: a cross-sectional survey of two districts in Uganda.

    Science.gov (United States)

    Rukundo, Peter M; Iversen, Per O; Andreassen, Bård A; Oshaug, Arne; Kikafunda, Joyce; Rukooko, Byaruhanga

    2015-04-25

    Despite the instruments on the right to adequate food adopted by the United Nations, there exists limited information on how this right is perceived. Following a major 2010 landslide disaster in the Bududa district of Eastern Uganda and the resettlement of some affected households into the Kiryandongo district in Western Uganda, we surveyed both districts to explore perceptions about the right to adequate food among households with different experiences; disaster-affected and controls. We deployed qualitative and quantitative techniques to a cross-sectional survey. The index respondent was the head of each randomly selected household from the landslide affected communities and controls from a bordering sub-county. Data was collected by interviews and focus group discussions (FGDs). Structured entries were tested statistically to report associations using Pearson's Chi-square at the 95% CI. Information from FGDs was transcribed, coded, sequenced and patterned. Findings from both techniques were triangulated to facilitate interpretations. Analysis included 1,078 interview entries and 12 FGDs. Significant differences between the affected and control households (P landslide displacement and resettlement. Information materials need to be assembled and disseminated to stimulate awareness and debate on the right to adequate food.

  15. Assessment of medical students' proficiency in dermatology: Are medical students adequately prepared to diagnose and treat common dermatologic conditions in the United States?

    Science.gov (United States)

    Ulman, Catherine A; Binder, Stephen Bruce; Borges, Nicole J

    2015-01-01

    This study assessed whether a current medical school curriculum is adequately preparing medical students to diagnose and treat common dermatologic conditions. A 15-item anonymous multiple choice quiz covering fifteen diseases was developed to test students' ability to diagnose and treat common dermatologic conditions. The quiz also contained five items that assessed students' confidence in their ability to diagnose common dermatologic conditions, their perception of whether they were receiving adequate training in dermatology, and their preferences for additional training in dermatology. The survey was performed in 2014, and was completed by 85 students (79.4%). Many students (87.6%) felt that they received inadequate training in dermatology during medical school. On average, students scored 46.6% on the 15-item quiz. Proficiency at the medical school where the study was performed is considered an overall score of greater than or equal to 70.0%. Students received an average score of 49.9% on the diagnostic items and an average score of 43.2% on the treatment items. The findings of this study suggest that United States medical schools should consider testing their students and assessing whether they are being adequately trained in dermatology. Then schools can decide if they need to re-evaluate the timing and delivery of their current dermatology curriculum, or whether additional curriculum hours or clinical rotations should be assigned for dermatologic training.

  16. Assessment of medical students’ proficiency in dermatology: Are medical students adequately prepared to diagnose and treat common dermatologic conditions in the United States?

    Directory of Open Access Journals (Sweden)

    Catherine A. Ulman

    2015-05-01

    Full Text Available This study assessed whether a current medical school curriculum is adequately preparing medical students to diagnose and treat common dermatologic conditions. A 15-item anonymous multiple choice quiz covering fifteen diseases was developed to test students’ ability to diagnose and treat common dermatologic conditions. The quiz also contained five items that assessed students’ confidence in their ability to diagnose common dermatologic conditions, their perception of whether they were receiving adequate training in dermatology, and their preferences for additional training in dermatology. The survey was performed in 2014, and was completed by 85 students (79.4%. Many students (87.6% felt that they received inadequate training in dermatology during medical school. On average, students scored 46.6% on the 15-item quiz. Proficiency at the medical school where the study was performed is considered an overall score of greater than or equal to 70.0%. Students received an average score of 49.9% on the diagnostic items and an average score of 43.2% on the treatment items. The findings of this study suggest that United States medical schools should consider testing their students and assessing whether they are being adequately trained in dermatology. Then schools can decide if they need to re-evaluate the timing and delivery of their current dermatology curriculum, or whether additional curriculum hours or clinical rotations should be assigned for dermatologic training.

  17. The effects of sonographic and demographic features and needle size on obtaining adequate cytological material in sonography-guided fine-needle aspiration biopsy of thyroid nodules.

    Science.gov (United States)

    İnci, Mehmet Fatih; Özkan, Fuat; Yüksel, Mürvet; Şalk, İsmail; Şahin, Murat

    2013-04-01

    The aim of this study is to investigate the effects of the sonographic characteristics of the nodule, demographic features of patient, and nodule size and needle size used for sampling, on obtaining adequate cytological material (CM) in thyroid fine-needle aspiration biopsy (FNAB). We performed 270 FNAB between September 2010 and June 2012. Size, echogenicity, and localization of all nodules were evaluated by ultrasonography (US) before the biopsy. Nodules were grouped as 3 cm according to their size and as hypoechoic, isoechoic, hyperechoic, or heterogeneous according to their US characteristics. 20-, 22-, and 24-G needles were used for the biopsies. Different sonographic characteristics of the nodules did not affect the needle selection. All specimens were classified as adequate or inadequate CM by a cytopathologist. A total of 270 nodules were biopsied, 184 (68.1 %) specimens were considered as adequate CM and 86 (31.9 %) specimens were considered as inadequate CM. Patient age and the presence of heterogeneous echogenicity were found to have prognostic significance in univariate analysis (p 3 cm and needle size 20-G usage) and variables found to be statistically significant in univariate analysis. Non-diagnostic FNAB remains a significant problem in the evaluation of thyroid nodules and can be as high as 30 %. Inadequate CM rates for elderly patients and heterogeneous nodules were significantly higher than that for other factors. The nodule size and needle size used for sampling did not affect the adequacy of FNAB.

  18. Assessment of medical students’ proficiency in dermatology: Are medical students adequately prepared to diagnose and treat common dermatologic conditions in the United States?

    Directory of Open Access Journals (Sweden)

    Catherine A Ulman

    2015-05-01

    Full Text Available This study assessed whether a current medical school curriculum is adequately preparing medical students to diagnose and treat common dermatologic conditions. A 15-item anonymous multiple choice quiz covering fifteen diseases was developed to test students’ ability to diagnose and treat common dermatologic conditions. The quiz also contained five items that assessed students’ confidence in their ability to diagnose common dermatologic conditions, their perception of whether they were receiving adequate training in dermatology, and their preferences for additional training in dermatology. The survey was performed in 2014, and was completed by 85 students (79.4%. Many students (87.6% felt that they received inadequate training in dermatology during medical school. On average, students scored 46.6% on the 15-item quiz. Proficiency at the medical school where the study was performed is considered an overall score of greater than or equal to 70.0%. Students received an average score of 49.9% on the diagnostic items and an average score of 43.2% on the treatment items. The findings of this study suggest that United States medical schools should consider testing their students and assessing whether they are being adequately trained in dermatology. Then schools can decide if they need to re-evaluate the timing and delivery of their current dermatology curriculum, or whether additional curriculum hours or clinical rotations should be assigned for dermatologic training.

  19. Adequate prenatal care reduces the risk of adverse pregnancy outcomes in women with history of infertility: a nationwide population-based study.

    Directory of Open Access Journals (Sweden)

    Raushan Alibekova

    Full Text Available OBJECTIVES: To investigate the effects of various measures of prenatal care on adverse pregnancy outcomes in women with a history of infertility. STUDY DESIGN: A retrospective cohort study. METHODS: Data were derived by linking 2 large nationwide population-based datasets, the National Health Insurance Research Database and Taiwan Birth Certificate Registry. The study sample included 15,056 women with an infertility diagnosis and 60,224 randomly selected women without infertility matched to the study sample by maternal age. A conditional logistic regression analysis was performed for the analysis. RESULTS: Women diagnosed with infertility respectively had 1.39 (95% CI, 1.06~1.83, 1.15 (95% CI, 1.08~1.24, 1.13 (95% CI, 1.08~1.18, and 1.08 (95% CI, 1.05~1.12 higher odds of having very low birth weight (VLBW babies, preterm births, labor complications, and cesarean sections (CSs compared to women without infertility. Inadequate numbers of total and major prenatal visits and late initiation of prenatal care increased the risks of adverse pregnancy outcomes in women with infertility, especially the risk of a VLBW baby. However, no significant associations were found for the risks of adverse birth outcomes in infertile women with adequate prenatal care compared to fertile women with adequate care. CONCLUSIONS: Study findings suggest that adequate prenatal care can reduce the risk of adverse pregnancy outcomes in women with infertility.

  20. Adequate but not supplemental folic acid combined with soy isoflavones during early life improves bone health at adulthood in male mice.

    Science.gov (United States)

    Kaludjerovic, Jovana; Ward, Wendy E

    2013-10-01

    Previous investigations from our laboratory have demonstrated that neonatal exposure to soy isoflavones (ISO) improves bone outcomes in CD-1 mice at adulthood with greater benefits in females than males. This study determined whether early-life exposure to supplemental folic acid (FA) - that may enhance DNA methylation of target genes - in combination with ISO provides greater benefits to male bone development than ISO alone. CD-1 dams were randomized to a low (0 mg/kg diet), adequate (2 mg/kg diet) or supplemental (8 mg/kg diet) level of FA during pregnancy and lactation. Offspring received corn oil or ISO (7 mg/kg of body weight per day) from postnatal day 1-10. From weaning, males were fed adequate FA and studied to age 4 months. Offspring exposed to adequate FA+ISO had multiple benefits to bone health: higher (Pbenefits to male bone development, while improvements induced by supplemental FA+ISO were limited to a higher level of serum OPG. Mechanistic studies are needed to better understand how FA and ISO improve bone development in male offspring.