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

Structure and function of initiator methionine tRNA from the mitochondria of Neurospora crassa

International Nuclear Information System (INIS)

Heckman, J.E.; Hecker, L.I.; Schwartzbach, S.D.; Barnett, W.E.; Baumstark, B.; RajBhandary, U.L.

1978-01-01

Initiator methionine tRNA from the mitochondria of Neurospora crassa has been purified and sequenced. This mitochondrial tRNA can be aminoacylated and formylated by E. coli enzymes, and is capable of initiating protein synthesis in E. coli extracts. The nucleotide composition of the mitochondrial initiator tRNA (the first mitochondrial tRNA subjected to sequence analysis) is very rich in A + U, like that reported for total mitochondrial tRNA. In two of the unique features which differentiate procaryotic from eucaryotic cytoplasmic initiator tRNAs, the mitochondrial tRNA appears to resemble the eucaryotic initiator tRNAs. Thus unlike procaryotic initiator tRNAs in which the 5' terminal nucleotide cannot form a Watson-Crick base pair to the fifth nucleotide from 3' end, the mitochondrial tRNA can form such a base pair; and like the eucaryotic cytoplasmic initiator tRNAs, the mitochondrial initiator tRNA lacks the sequence - T psiCG(or A) in loop IV. The corresponding sequence in the mitochondrial tRNA, however, is -UGCA- and not -AU(or psi)CG- as found in all eucaryotic cytoplasmic initiator tRNAs. In spite of some similarity of the mitochondrial initiator tRNA to both eucaryotic and procaryotic initiator tRNAs, the mitochondrial initiator tRNA is basically different from both these tRNAs. Between these two classes of initiator tRNAs, however, it is more homologous in sequence to procaryotic (56 to 60%) than to eucaryotic cytoplasmic initiator tRNAs

Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA.

Science.gov (United States)

Chu, Xiang-Qiang; Mamontov, Eugene; O'Neill, Hugh; Zhang, Qiu

2013-03-21

The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.

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.

Mitochondrial tRNA gene translocations in highly eusocial bees

Directory of Open Access Journals (Sweden)

Daniela Silvestre

2006-01-01

Full Text Available Mitochondrial gene rearrangement events, especially involving tRNA genes, have been described more frequently as more complete mitochondrial genome sequences are becoming available. In the present work, we analyzed mitochondrial tRNA gene rearrangements between two bee species belonging to the tribes Apini and Meliponini within the "corbiculate Apidae". Eleven tRNA genes are in different genome positions or strands. The molecular events responsible for each translocation are explained. Considering the high number of rearrangements observed, the data presented here contradict the general rule of high gene order conservation among closely related organisms, and also represent a powerful molecular tool to help solve questions about phylogeny and evolution in bees.

Overexpressing both ATP sulfurylase and selenocysteine methyltransferase enhances selenium phytoremediation traits in Indian mustard

International Nuclear Information System (INIS)

LeDuc, Danika L.; AbdelSamie, Manal; Montes-Bayon, Maria; Wu, Carol P.; Reisinger, Sarah J.; Terry, Norman

2006-01-01

A major goal of our selenium (Se) phytoremediation research is to use genetic engineering to develop fast-growing plants with an increased ability to tolerate, accumulate, and volatilize Se. To this end we incorporated a gene (encoding selenocysteine methyltransferase, SMT) from the Se hyperaccumulator, Astragalus bisulcatus, into Indian mustard (LeDuc, D.L., Tarun, A.S., Montes-Bayon, M., Meija, J., Malit, M.F., Wu, C.P., AbdelSamie, M., Chiang, C.-Y., Tagmount, A., deSouza, M., Neuhierl, B., Boeck, A., Caruso, J., Terry, N., 2004. Overexpression of selenocysteine methyltransferase in Arabidopsis and Indian mustard increases selenium tolerance and accumulation Plant Physiol. 135, 377-383.). The resulting transgenic plants successfully enhanced Se phytoremediation in that the plants tolerated and accumulated Se from selenite significantly better than wild type. However, the advantage conferred by the SMT enzyme was much less when Se was supplied as selenate. In order to enhance the phytoremediation of selenate, we developed double transgenic plants that overexpressed the gene encoding ATP sulfurylase (APS) in addition to SMT, i.e., APS x SMT. The results showed that there was a substantial improvement in Se accumulation from selenate (4 to 9 times increase) in transgenic plants overexpressing both APS and SMT. - Simultaneous overexpression of APS and SMT genes in Indian mustard greatly increases ability to accumulate selenate

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.

tRNA modification profiles of the fast-proliferating cancer cells

International Nuclear Information System (INIS)

Dong, Chao; Niu, Leilei; Song, Wei; Xiong, Xin; Zhang, Xianhua; Zhang, Zhenxi; Yang, Yi; Yi, Fan; Zhan, Jun; Zhang, Hongquan; Yang, Zhenjun; Zhang, Li-He; Zhai, Suodi; Li, Hua; Ye, Min; Du, Quan

2016-01-01

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.

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 ...File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg_trna.zip File size: 1 KB Simple search URL http:...ption Download License Update History of This Database Site Policy | Contact Us tRNA - RMG | LSDB Archive ...

Resolution of oxidative stress by thioredoxin reductase: Cysteine versus selenocysteine

Directory of Open Access Journals (Sweden)

Brian Cunniff

2014-01-01

Full Text Available Thioredoxin reductase (TR catalyzes the reduction of thioredoxin (TRX, which in turn reduces mammalian typical 2-Cys peroxiredoxins (PRXs 1–4, thiol peroxidases implicated in redox homeostasis and cell signaling. Typical 2-Cys PRXs are inactivated by hyperoxidation of the peroxidatic cysteine to cysteine-sulfinic acid, and regenerated in a two-step process involving retro-reduction by sulfiredoxin (SRX and reduction by TRX. Here transient exposure to menadione and glucose oxidase was used to examine the dynamics of oxidative inactivation and reactivation of PRXs in mouse C10 cells expressing various isoforms of TR, including wild type cytoplasmic TR1 (Sec-TR1 and mitochondrial TR2 (Sec-TR2 that encode selenocysteine, as well as mutants of TR1 and TR2 in which the selenocysteine codon was changed to encode cysteine (Cys-TR1 or Cys-TR2. In C10 cells endogenous TR activity was insensitive to levels of hydrogen peroxide that hyperoxidize PRXs. Expression of Sec-TR1 increased TR activity, reduced the basal cytoplasmic redox state, and increased the rate of reduction of a redox-responsive cytoplasmic GFP probe (roGFP, but did not influence either the rate of inactivation or the rate of retro-reduction of PRXs. In comparison to roGFP, which was reduced within minutes once oxidants were removed reduction of 2-Cys PRXs occurred over many hours. Expression of wild type Sec-TR1 or Sec-TR2, but not Cys-TR1 or TR2, increased the rate of reduction of PRXs and improved cell survival after menadione exposure. These results indicate that expression levels of TR do not reduce the severity of initial oxidative insults, but rather govern the rate of reduction of cellular factors required for cell viability. Because Sec-TR is completely insensitive to cytotoxic levels of hydrogen peroxide, we suggest TR functions at the top of a redox pyramid that governs the oxidation state of peroxiredoxins and other protein factors, thereby dictating a hierarchy of phenotypic

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.

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.

Science.gov (United States)

Fischer, Niels; Konevega, Andrey L; Wintermeyer, Wolfgang; Rodnina, Marina V; Stark, Holger

2010-07-15

The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.

Comparative study on the bioactivation mechanisms and cytotoxicity of Te-phenyl-L-tellurocysteine, Se-phenyl-L-selenocysteine, and S-phenyl-L-cysteine

NARCIS (Netherlands)

Rooseboom, Martijn; Vermeulen, Nico P E; Durgut, Fatma; Commandeur, Jan N M

2002-01-01

Tellurium compounds are effective antioxidants and chemoprotectors, even more active than their selenium and sulfur analogues. In addition to these properties, some selenium compounds, such as selenocysteine Se-conjugates, possess significant chemopreventive and antitumor activities, and selenol

tRNA's wobble decoding of the genome: 40 years of modification.

Science.gov (United States)

Agris, Paul F; Vendeix, Franck A P; Graham, William D

2007-02-09

The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA's wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick's Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3'-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins.

Selenocysteine in thiol/disulfide-like exchange reactions.

Science.gov (United States)

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.

The early history of tRNA recognition by aminoacyl-tRNA synthetases

Indian Academy of Sciences (India)

Madhu

2006-10-04

Oct 4, 2006 ... Discovery of aminoacyl-tRNA synthetases and importance ... The pioneering work of Fritz Lipmann on the high-energy ... the peculiar structural and functional relationships tRNAs ... a bulk of only 20 families of tRNA molecules in contrast ...... balance of tRNA and aminoacyl-tRNA synthetase; Science 242.

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.

The fractionation of t-RNA on N,N′-bis(3-aminopropyl)-piperazine substituted-Sepharose

Science.gov (United States)

Leberman, Reuben; Giovanelli, Ruth; Acosta, Zenobio

1974-01-01

An anion exchange agarose has been prepared by modifying sepharose 6B with N,N′-bis (-3-aminopropyl) piperazine. This material (BAPP-Sepharose) has been used for the fractionation of t-RNA from E.coli by column chromatography. The results obtained with gram quantities of crude t-RNA at pH 4.6 and pH 8.0 as measured by the elution patterns of alanyl, arginyl, aspartyl, leucyl, lysyl, methionyl, phenylalanyl, prolyl, seryl, tyrosyl, and valyl t-RNA are described. PMID:10793731

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

2013-08-01

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.

Sharing the load: Mex67-Mtr2 cofunctions with Los1 in primary tRNA nuclear export.

Science.gov (United States)

Chatterjee, Kunal; Majumder, Shubhra; Wan, Yao; Shah, Vijay; Wu, Jingyan; Huang, Hsiao-Yun; Hopper, Anita K

2017-11-01

Eukaryotic transfer RNAs (tRNAs) are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function for protein synthesis. The evolutionarily conserved β-importin family member Los1 (Exportin-t) has been the only exporter known to execute nuclear export of newly transcribed intron-containing pre-tRNAs. Interestingly, LOS1 is unessential in all tested organisms. As tRNA nuclear export is essential, we previously interrogated the budding yeast proteome to identify candidates that function in tRNA nuclear export. Here, we provide molecular, genetic, cytological, and biochemical evidence that the Mex67-Mtr2 (TAP-p15) heterodimer, best characterized for its essential role in mRNA nuclear export, cofunctions with Los1 in tRNA nuclear export. Inactivation of Mex67 or Mtr2 leads to rapid accumulation of end-matured unspliced tRNAs in the nucleus. Remarkably, merely fivefold overexpression of Mex67-Mtr2 can substitute for Los1 in los1 Δ cells. Moreover, in vivo coimmunoprecipitation assays with tagged Mex67 document that the Mex67 binds tRNAs. Our data also show that tRNA exporters surprisingly exhibit differential tRNA substrate preferences. The existence of multiple tRNA exporters, each with different tRNA preferences, may indicate that the proteome can be regulated by tRNA nuclear export. Thus, our data show that Mex67-Mtr2 functions in primary nuclear export for a subset of yeast tRNAs. © 2017 Chatterjee et al.; Published by Cold Spring Harbor Laboratory Press.

Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase.

Science.gov (United States)

Muruganandam, Gopinath; Raasakka, Arne; Myllykoski, Matti; Kursula, Inari; Kursula, Petri

2017-05-16

Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering. We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain.

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...

Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation.

Science.gov (United States)

Agarwal, Shweta; Tyagi, Gunjan; Chadha, Deepti; Mehrotra, Ranjana

2017-01-01

Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (K a ) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×10 2 M -1 , 4.923×10 2 M -1 and 4.223×10 2 M -1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and

Viral tRNA Mimicry from a Biocommunicative Perspective

Directory of Open Access Journals (Sweden)

Ascensión Ariza-Mateos

2017-12-01

Full Text Available RNA viruses have very small genomes which limits the functions they can encode. One of the strategies employed by these viruses is to mimic key factors of the host cell so they can take advantage of the interactions and activities these factors typically participate in. The viral RNA genome itself was first observed to mimic cellular tRNA over 40 years ago. Since then researchers have confirmed that distinct families of RNA viruses are accessible to a battery of cellular factors involved in tRNA-related activities. Recently, potential tRNA-like structures have been detected within the sequences of a 100 mRNAs taken from human cells, one of these being the host defense interferon-alpha mRNA; these are then additional to the examples found in bacterial and yeast mRNAs. The mimetic relationship between tRNA, cellular mRNA, and viral RNA is the central focus of two considerations described below. These are subsequently used as a preface for a final hypothesis drawing on concepts relating to mimicry from the social sciences and humanities, such as power relations and creativity. Firstly, the presence of tRNA-like structures in mRNAs indicates that the viral tRNA-like signal could be mimicking tRNA-like elements that are contextualized by the specific carrier mRNAs, rather than, or in addition to, the tRNA itself, which would significantly increase the number of potential semiotic relations mediated by the viral signals. Secondly, and in particular, mimicking a host defense mRNA could be considered a potential new viral strategy for survival. Finally, we propose that mRNA’s mimicry of tRNA could be indicative of an ancestral intracellular conflict in which species of mRNAs invaded the cell, but from within. As the meaning of the mimetic signal depends on the context, in this case, the conflict that arises when the viral signal enters the cell can change the meaning of the mRNAs’ internal tRNA-like signals, from their current significance to that

Catalytic mechanism and inhibition of tRNA (Uracil-5-)methyltransferase: evidence for covalent catalysis

International Nuclear Information System (INIS)

Santi, D.V.; Hardy, L.W.

1987-01-01

tRNA (Ura-5-) methyltransferase catalyzes the transfer of a methyl group from S-adenosylmethionine (AdoMet) to the 5-carbon of a specific Urd residue in tRNA. This results in stoichiometric release of tritium from [5- 3 H] Urd-labeled substrate tRNA isolated from methyltransferase-deficient Escherichia coli. The enzyme also catalyzes an AdoMet-independent exchange reaction between [5- 3 H]-Urd-labeled substrate tRNA and protons of water at a rate that is about 1% that of the normal methylation reaction, but with identical stoichiometry. S-Adenosylhomocysteine inhibits the rate of the exchange reaction by 2-3-fold, whereas an analog having the sulfur of AdoMet replaced by nitrogen accelerates the exchange reaction 9-fold. In the presence (but not absence) of AdoMet, 5-fluorouracil-substituted tRNA (FUra-tRNA) leads to the first-order inactivation of the enzyme. This is accompanied by the formation of a stable covalent complex containing the enzyme, FUra-tRNA, and the methyl group AdoMet. A mechanism for catalysis is proposed that explains both the 5-H exchange reaction and the inhibition by FUra-tRNA: the enzyme forms a covalent Michael adduct with substrate or inhibitor tRNA by attack of a nucleophilic group of the enzyme at carbon 6 of the pyrimidine residue to be modified. As a result, an anion equivalent is generated at carbon 5 that is sufficiently reactive to be methylated by AdoMet. Preliminary experiments and precedents suggest that the nucleophilic catalyst of the enzyme is a thiol group of cysteine. The potent irreversible inhibition by FUra-tRNA suggest that a mechanism for the RNA effects of FUra may also involve irreversible inhibition of RNA-modifying enzymes

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.

Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.

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Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V

2007-04-01

During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.

The effect of tRNA levels on decoding times of mRNA codons.

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Dana, Alexandra; Tuller, Tamir

2014-08-01

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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Carter, Charles W.; Wolfenden, Richard

2016-01-01

abstract 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. PMID:26595350

Structural requirements for the binding of tRNA Lys3 to reverse transcriptase of the human immunodeficiency virus type 1

NARCIS (Netherlands)

Oude Essink, B. B.; Das, A. T.; Berkhout, B.

1995-01-01

Reverse transcription of the human immunodeficiency virus type 1 (HIV-1) RNA genome is primed by the cellular tRNA Lys3 molecule. Packaging of this tRNA primer during virion assembly is thought to be mediated by specific interactions with the reverse transcriptase (RT) protein. Portions of the tRNA

Direct application of radioiodinated aminoacyl tRNA for radiolabeling nascent proteins

International Nuclear Information System (INIS)

Scherberg, N.H.; Barokas, K.; Murata, Y.; Refetoff, S.

1985-01-01

A two-step procedure to incorporate 125 I-iodotyrosine into protein synthesized in a reticulocyte lysate is described. In the first step, the iodination of tyrosyl tRNA was catalyzed by a solid-state glycouril compound. More than one-third of 200 microCi of radioiodine became bound to 70 micrograms of aminoacyl tRNA after 15 min at 0 degrees C. The isotope was distributed in a three-to-one ratio of monoiodotyrosine to di-iodotyrosine. In the second step, the soluble product of the radioiodination was transferred directly into a nuclease-treated reticulocyte lysate coded with RNA isolated from the human hepatoma cell line Hep G2. Fractional recovery of radioiodine in nascent protein was maximally 7.6%. Reaction of the product of translation with antibody against alpha-antitrypsin separated an 125 I-containing protein having a molecular weight estimated as 47,000. The synthesis of unprocessed alpha-antitrypsin was confirmed by cleavage of the labeled protein with leader peptidase and by its displacement from immunocomplex formation with purified alpha-antitrypsin. The amount of 125 I incorporated into alpha-antitrypsin was proportionate to iodinated tRNA additions up to a concentration of 70 micrograms/ml. The synthesis of alpha-antitrypsin as detected in radioautograms after gel electrophoresis was more than twice as sensitive using radioiodinated aminoacyl tRNA as compared with [ 35 S]methionine. Iodine labeling of thyroxine-binding globulin was also demonstrated in the translation product of Hep G2 RNA. Since the specific activity of the radioiodine is high and the means for detection of the isotope efficient, the method described can facilitate the demonstration of quantitatively minor translation products

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.

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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.

Conformation and functioning of tRNAs: cross-linked tRNAs as substrate for tRNA nucleotidyl-transferase and aminoacyl synthetases

International Nuclear Information System (INIS)

Carre, D.S.; Thomas, G.; Favre, A.

1974-01-01

The behavior of mixed E. coli tRNAs ''cross-linked'' by irradiation with near ultraviolet light (310-400 nm) has been compared to that of the intact molecules in two enzymatic processes. No change in the rate and extent of the repair of the pCpCpA 3' terminus of tRNA by purified E. coli tRNA nucleotidyltransferase can be detected. In contrast, complex data were obtained in the acylation reaction. They can be understood using other tRNA specific modifications as well as our present knowledge of E. coli tRNA sequences and rare base content [fr

Identification of Aquifex aeolicus tRNA (m2(2G26) methyltransferase gene.

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Takeda, Hiroshi; Hori, Hiroyuki; Endo, Yaeta

2002-01-01

The modifications of N2,N2-dimethylguanine (m2(2)G) are found in tRNAs and rRNAs from eukarya and archaea. In tRNAs, modification at position G26 is generated by tRNA (m2(2)G26) methyltransferase, which is encoded by the corresponding gene, trm1. This enzyme catalyzes the methyl-transfer from S-adenosyl-L-methionine to the semi-conserved residue, G26, via the intermediate modified base, m2G26. Recent genome sequencing project has been reported that the putative trm1 is encoded in the genome of Aquifex aeolicus, a hyper-thermophilic eubacterium as only one exception among eubacteria. In order to confirm whether this bacterial trm1 gene product is a real tRNA (m2(2)G26) methyltransferase or not, we expressed this protein by wheat germ in vitro cell-free translation system. Our biochemical analysis clearly showed that this gene product possessed tRNA (m2(2)G26) methyltransferase activity.

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

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Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

2016-09-14

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

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

International Nuclear Information System (INIS)

Miyagawa, Ryu; Mizuno, Rie; Watanabe, Kazunori; Ijiri, Kenichi

2012-01-01

Highlights: ► tRNAs are tranlocated into the nucleus in heat-induced HeLa cells. ► tRNAs form the unique granules in the nucleus. ► 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 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 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.

Deletion analysis of the expression of rRNA genes and associated tRNA genes carried by a lambda transducing bacteriophage

International Nuclear Information System (INIS)

Morgan, E.A.; Nomura, M.

1979-01-01

Transducing phage lambda ilv5 carries genes for rRNA's, spacer tRNA's (tRNA 1 /sup Ile/ and tRNA/sub 1B//sup Ala/), and two other tRNA's (tRNA 1 /sup Asp/ and tRNA/sup Trp/). We have isolated a mutant of lambda ilv5, lambda ilv5su7, which carries an amber suppressor mutation in the tRNA/sup Trp/ gene. A series of deletion mutants were isolated from the lambda ilv5su7 phage. Genetic and biochemical analyses of these deletion mutants have confirmed our previous conclusion that the genes for tRNA 1 /sup Asp/ and tRNA/sup Trp/ located at the distal end of the rRNA operon (rrnC) are cotranscribed with other rRNA genes in that operon. In addition, these deletions were used to define roughly the physical location of the promoter(s) of the rRNA operon carried by the lambda ilv5su7 transducing phage

Crosslinking of tRNA containing a long extra arm to elongation factor Tu by trans-diamminedichloroplatinum(II)

DEFF Research Database (Denmark)

Rasmussen, Nils-Jørgen; Wikman, Friedrik; Clark, Brian F. C.

1990-01-01

A tRNA containing a long extra arm, namely E. coli tRNA1Leu has been crosslinked to elongation factor Tu, with the crosslinking reagent trans-diamminedichloroplatinum(II). The nucleotide involved in the crosslinking was identified to be a guanosine in the variable region at position 47F or 47G....

Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis.

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Ferro, Iolanda; Liebeton, Klaus; Ignatova, Zoya

2017-10-13

Cellular growth crucially depends on protein synthesis and the abundance of translational components. Among them, aminoacyl-tRNAs play a central role in biosynthesis and shape the kinetics of mRNA translation, thus influencing protein production. Here, we used microarray-based approaches to determine the charging levels and tRNA abundance of Bacillus licheniformis. We observed an interesting cross-talk among tRNA expression, charging pattern, and growth rate. For a large subset of tRNAs, we found a co-regulated and augmented expression at high growth rate. Their tRNA aminoacylation level is kept relatively constant through riboswitch-regulated expression of the cognate aminoacyl-tRNA-synthetase (AARS). We show that AARSs with putative riboswitch-controlled expression are those charging tRNAs with amino acids which disfavor cell growth when individually added to the nutrient medium. Our results suggest that the riboswitch-regulated AARS expression in B. licheniformis is a powerful mechanism not only to maintain a constant ratio of aminoacyl-tRNA independent of the growth rate but concomitantly to control the intracellular level of free amino acids. Copyright © 2017 Elsevier Ltd. All rights reserved.

The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules.

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Aldinger, Carolin A; Leisinger, Anne-Katrin; Gaston, Kirk W; Limbach, Patrick A; Igloi, Gabor L

2012-10-01

It is a prevalent concept that, in line with the Wobble Hypothesis, those tRNAs having an adenosine in the first position of the anticodon become modified to an inosine at this position. Sequencing the cDNA derived from the gene coding for cytoplasmic tRNA (Arg) ACG from several higher plants as well as mass spectrometric analysis of the isoacceptor has revealed that for this kingdom an unmodified A in the wobble position of the anticodon is the rule rather than the exception. In vitro translation shows that in the plant system the absence of inosine in the wobble position of tRNA (Arg) does not prevent decoding. This isoacceptor belongs to the class of tRNA that is imported from the cytoplasm into the mitochondria of higher plants. Previous studies on the mitochondrial tRNA pool have demonstrated the existence of tRNA (Arg) ICG in this organelle. In moss the mitochondrial encoded distinct tRNA (Arg) ACG isoacceptor possesses the I34 modification. The implication is that for mitochondrial protein biosynthesis A-to-I editing is necessary and occurs by a mitochondrion-specific deaminase after import of the unmodified nuclear encoded tRNA (Arg) ACG.

Early days of tRNA research: Discovery, function, purification and ...

Indian Academy of Sciences (India)

Madhu

2006-10-04

Oct 4, 2006 ... function in protein synthesis and methods for its purification ... intermediate carrier of the amino acid in protein synthesis. (table 1). .... 14C-leucine were incubated with GTP, PEP, and pyruvate kinase as indicated (adapted from: Hoagland et al 1958). .... Purification of N. crassa mitochondrial initiator tRNA.

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.

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

The uropathogenic Escherichia coli strain 536 (06:K15:H31) carries two large chromosomalpathogenicity islands (Pais). Both Pais are flanked by tRNA genes. Spontaneous deletion of Pai IIresults in truncation of the leuX tRNA5Leu gene. This tRNA is required for the expression of type 1fimbriae (Fim...

Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.

Science.gov (United States)

Zhang, Yan; Hong, Samuel; Ruangprasert, Ajchareeya; Skiniotis, Georgios; Dunham, Christine M

2018-03-06

Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. Copyright © 2018 Elsevier Ltd. All rights reserved.

DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA.

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Govindaraju, Gayathri; Jabeena, C A; Sethumadhavan, Devadathan Valiyamangalath; Rajaram, Nivethika; Rajavelu, Arumugam

2017-10-01

In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite. Copyright © 2017 Elsevier B.V. All rights reserved.

Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

International Nuclear Information System (INIS)

Kim, Moon-Jung; Lee, Byung Cheon; Hwang, Kwang Yeon; Gladyshev, Vadim N.; Kim, Hwa-Young

2015-01-01

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. 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 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

Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

Energy Technology Data Exchange (ETDEWEB)

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.

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.

Snapshots of Dynamics in Synthesizing N6-isopentenyladenosine at tRNA Anticodon†,‡

Science.gov (United States)

Chimnaronk, Sarin; Forouhar, Farhad; Sakai, Junichi; Yao, Min; Tron, Cecile M.; Atta, Mohamed; Fontecave, Marc; Hunt, John F.; Tanaka, Isao

2009-01-01

Bacterial and eukaryotic transfer RNAs that decode codons starting with uridine have a hydrophobically-hypermodified adenosine at the position 37 (A37) adjacent to the 3′-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of the crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during modification of RNA. A compact evolutionary inserted domain (herein ‘swinging domain’) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A36 and A38 together to squeeze out A37 into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate-binding of MiaA. PMID:19435325

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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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.

Interaction of tRNA with Eukaryotic Ribosome

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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.

tRNA Is the Source of Low-Level trans-Zeatin Production in Methylobacterium spp.†‡

Science.gov (United States)

Koenig, Robbin L.; Morris, Roy O.; Polacco, Joe C.

2002-01-01

Pink-pigmented facultatively methylotrophic bacteria (PPFMs), classified as Methylobacterium spp., are persistent colonizers of plant leaf surfaces. Reports of PPFM-plant dialogue led us to examine cytokinin production by PPFMs. Using immunoaffinity and high-performance liquid chromatography (HPLC) purification, we obtained 22 to 111 ng of trans-zeatin per liter from culture filtrates of four PPFM leaf isolates (from Arabidopsis, barley, maize, and soybean) and of a Methylobacterium extorquens type culture originally recovered as a soil isolate. We identified the zeatin isolated as the trans isomer by HPLC and by a radioimmunoassay in which monoclonal antibodies specific for trans-hydroxylated cytokinins were used. Smaller and variable amounts of trans-zeatin riboside were also recovered. trans-Zeatin was recovered from tRNA hydrolysates in addition to the culture filtrates, suggesting that secreted trans-zeatin resulted from tRNA turnover rather than from de novo synthesis. The product of the miaA gene is responsible for isopentenylation of a specific adenine in some tRNAs. To confirm that the secreted zeatin originated from tRNA, we mutated the miaA gene of M. extorquens by single exchange of an internal miaA fragment into the chromosomal gene. Mutant exconjugants, confirmed by PCR, did not contain zeatin in their tRNAs and did not secrete zeatin into the medium, findings which are consistent with the hypothesis that all zeatin is tRNA derived rather than synthesized de novo. In germination studies performed with heat-treated soybean seeds, cytokinin-null (miaA) mutants stimulated germination as well as wild-type bacteria. While cytokinin production may play a role in the plant-PPFM interaction, it is not responsible for stimulation of germination by PPFMs. PMID:11889088

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Science.gov (United States)

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

2018-03-01

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.

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Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

Effects of Heterologous tRNA Modifications on the Production of Proteins Containing Noncanonical Amino Acids

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Ana Crnković

2018-02-01

Full Text Available Synthesis of proteins with noncanonical amino acids (ncAAs enables the creation of protein-based biomaterials with diverse new chemical properties that may be attractive for material science. Current methods for large-scale production of ncAA-containing proteins, frequently carried out in Escherichia coli, involve the use of orthogonal aminoacyl-tRNA synthetases (o-aaRSs and tRNAs (o-tRNAs. Although o-tRNAs are designed to be orthogonal to endogenous aaRSs, their orthogonality to the components of the E. coli metabolism remains largely unexplored. We systematically investigated how the E. coli tRNA modification machinery affects the efficiency and orthogonality of o-tRNASep used for production of proteins with the ncAA O-phosphoserine (Sep. The incorporation of Sep into a green fluorescent protein (GFP in 42 E. coli strains carrying deletions of single tRNA modification genes identified several genes that affect the o-tRNA activity. Deletion of cysteine desulfurase (iscS increased the yield of Sep-containing GFP more than eightfold, while overexpression of dimethylallyltransferase MiaA and pseudouridine synthase TruB improved the specificity of Sep incorporation. These results highlight the importance of tRNA modifications for the biosynthesis of proteins containing ncAAs, and provide a novel framework for optimization of o-tRNAs.

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

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

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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.

T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions

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Sherwood, Anna V.; Grundy, Frank J.; Henkin, Tina M.

2015-01-01

The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5′ untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNA-dependent stabilization of a helix that sequesters a sequence complementary to the Shine–Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNAIle and tRNAIle-dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch. PMID:25583497

Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks.

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Wei, Fangping; Chen, Bowen

2012-03-01

To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.

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

International Nuclear Information System (INIS)

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

1986-01-01

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

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

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...... 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...

Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator.

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Mehlgarten, Constance; Prochaska, Heike; Hammermeister, Alexander; Abdel-Fattah, Wael; Wagner, Melanie; Krutyhołowa, Rościsław; Jun, Sang Eun; Kim, Gyung-Tae; Glatt, Sebastian; Breunig, Karin D; Stark, Michael J R; Schaffrath, Raffael

2017-09-05

Saccharomyces cerevisiae cells are killed by zymocin, a tRNase ribotoxin complex from Kluyveromyces lactis , which cleaves anticodons and inhibits protein synthesis. Zymocin's action requires specific chemical modification of uridine bases in the anticodon wobble position (U34) by the Elongator complex (Elp1-Elp6). Hence, loss of anticodon modification in mutants lacking Elongator or related KTI ( K. lactis Toxin Insensitive) genes protects against tRNA cleavage and confers resistance to the toxin. Here, we show that zymocin can be used as a tool to genetically analyse KTI12 , a gene previously shown to code for an Elongator partner protein. From a kti12 mutant pool of zymocin survivors, we identify motifs in Kti12 that are functionally directly coupled to Elongator activity. In addition, shared requirement of U34 modifications for nonsense and missense tRNA suppression ( SUP4 ; SOE1 ) strongly suggests that Kti12 and Elongator cooperate to assure proper tRNA functioning. We show that the Kti12 motifs are conserved in plant ortholog DRL1/ELO4 from Arabidopsis thaliana and seem to be involved in binding of cofactors (e.g., nucleotides, calmodulin). Elongator interaction defects triggered by mutations in these motifs correlate with phenotypes typical for loss of U34 modification. Thus, tRNA modification by Elongator appears to require physical contact with Kti12, and our preliminary data suggest that metabolic signals may affect proper communication between them.

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

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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.

Orthogonal use of a human tRNA synthetase active site to achieve multi-functionality

Science.gov (United States)

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B.; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A.; Schimmel, Paul; Yang, Xiang-Lei

2011-01-01

Protein multi-functionality is an emerging explanation for the complexity of higher organisms. In this regard, while aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, some also act in pathways for inflammation, angiogenesis, and apoptosis. How multiple functions evolved and their relationship to the active site is not clear. Here structural modeling analysis, mutagenesis, and cell-based functional studies show that the potent angiostatic, natural fragment of human TrpRS associates via Trp side chains that protrude from the cognate cellular receptor VE-cadherin. Modeling indicates that (I prefer the way it was because the conclusion was reached not only by modeling, but more so by experimental studies.)VE-cadherin Trp side chains fit into the Trp-specific active site of the synthetase. Thus, specific side chains of the receptor mimic (?) amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multi-functionality of human tRNA synthetases and other proteins. PMID:20010843

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

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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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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...

Affinity labeling of Escherichia coli phenylalanyl-tRNA synthetase at the binding site for tRNA

International Nuclear Information System (INIS)

Hountondji, C.; Schmitter, J.M.; Beauvallet, C.; Blanquet, S.

1987-01-01

Periodate-oxidized tRNA/sup Phe/ (tRNA/sub ox//sup Phe/) behaves as a specific affinity label of tetrameric Escherichia coli phenylalanyl-tRNA synthetase (PheRS). Reaction of the α 2 β 2 enzyme with tRNA/sub ox//sup Phe/ results in the loss of tRNA/sup Phe/ aminoacylation activity with covalent attachment of 2 mol of tRNA dialdehyde/mol of enzyme, in agreement with the stoichiometry of tRNA binding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the PheRS-[ 14 C]tRNA/sub ox//sup Phe/ covalent complex indicates that the large (α, M/sub r/ 87K) subunit of the enzyme interacts with the 3'-adenosine of tRNA/sub ox//sup Phe/. The [ 14 C]tRNA-labeled chymotryptic peptides of PheRS were purified by both gel filtration and reverse-phase high-performance liquid chromatography. The radioactivity was almost equally distributed among three peptides: Met-Lys[Ado]-Phe, Ala-Asp-Lys[Ado]-Leu, and Lys-Ile-Lys[Ado]-Ala. These sequences correspond to residues 1-3, 59-62, and 104-107, respectively, in the N-terminal region of the 795 amino acid sequence of the α subunit. It is noticeable that the labeled peptide Ala-Asp-Lys-Leu is adjacent to residues 63-66 (Arg-Val-Thr-Lys). The latter sequence was just predicted to resemble the proposed consensus tRNA CCA binding region Lys-Met-Ser-Lys-Ser, as deduced from previous affinity labeling studies on E. coli methionyl- and tyrosyl-tRNA synthetases

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.

Science.gov (United States)

Brok-Volchanskaya, Vera S; Kadyrov, Farid A; Sivogrivov, Dmitry E; Kolosov, Peter M; Sokolov, Andrey S; Shlyapnikov, Michael G; Kryukov, Valentine M; Granovsky, Igor E

2008-04-01

Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3' 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TpsiC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

Essential nontranslational functions of tRNA synthetases.

Science.gov (United States)

Guo, Min; Schimmel, Paul

2013-03-01

Nontranslational functions of vertebrate aminoacyl tRNA synthetases (aaRSs), which catalyze the production of aminoacyl-tRNAs for protein synthesis, have recently been discovered. Although these new functions were thought to be 'moonlighting activities', many are as critical for cellular homeostasis as their activity in translation. New roles have been associated with their cytoplasmic forms as well as with nuclear and secreted extracellular forms that affect pathways for cardiovascular development and the immune response and mTOR, IFN-γ and p53 signaling. The associations of aaRSs with autoimmune disorders, cancers and neurological disorders further highlight nontranslational functions of these proteins. New architecture elaborations of the aaRSs accompany their functional expansion in higher organisms and have been associated with the nontranslational functions for several aaRSs. Although a general understanding of how these functions developed is limited, the expropriation of aaRSs for essential nontranslational functions may have been initiated by co-opting the amino acid-binding site for another purpose.

Immunopurification of the suppressor tRNA dependent rabbit β-globin readthrough protein

International Nuclear Information System (INIS)

Hatfield, D.; Thorgeirsson, S.S.; Copeland, T.D.; Oroszlan, S.; Bustin, M.

1988-01-01

In mammalian cells, the rabbit β-globin readthrough protein is the only known example of a naturally occurring readthrough protein which does not involve a viral system. To provide an efficient means for its isolation, detection, and study, the authors elicited specific antibodies against this unique protein. The 22 amino acid peptide corresponding to the readthrough portion of this protein was synthesized, coupled to keyhole limpet hemocyanin, and injected into sheep. Specific antibodies to the peptide were produced as demonstrated by the enzyme-linked immunosorbent assay technique and by immunoblotting. The antibodies did not react with globin. The rabbit β-globin readthrough protein was separated from globin and other reticulocyte proteins by polyacrylamide gel electrophoresis and visualized by silver staining or by labeling with [ 35 S] methionine. Incorporation of [ 35 S] methionine into the readthrough protein was significantly enhanced upon addition of an opal suppressor tRNA to reticulocyte lysates. Immunoblotting revealed that the readthrough protein also occurs in lysates without added suppressor tRNA. The antibodies were purified on an affi-gel column which had been coupled with the peptide antigen. The readthrough protein was then purified from reticulocytes by immunoaffinity chromatography and by high-performance liquid chromatography. The results provide conclusive evidence that the β-globin readthrough protein is naturally occurring in rabbit reticulocytes

Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

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Ann E. Ehrenhofer-Murray

2017-02-01

Full Text Available Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA methyltransferases for cytosine-5 methylation, foremost C38 (m5C38 of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.

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

International Nuclear Information System (INIS)

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

2008-01-01

tRNA (m 7 G46) methyltransferase from E. coli was overexpressed, purified and crystallized. Diffraction data were collected to 2.04 Å resolution. 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

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.

Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

Directory of Open Access Journals (Sweden)

Hiraku Takada

Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

tRNA sequence data, annotation data and curation data - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

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Comparison of the redox chemistry of sulfur- and selenium-containing analogs of uracil✰

Science.gov (United States)

Payne, N. Connor; Geissler, Andrew; Button, Aileen; Sasuclark, Alexandru R.; Schroll, Alayne L.; Ruggles, Erik L.; Gladyshev, Vadim N.; Hondal, Robert J.

2017-01-01

Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNAGlu, tRNAGln and tRNALys. It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen. Both selenocysteine and 2-selenouridine have widespread analogs, cysteine and thiouridine, where sulfur is used instead. To examine the role of selenium in 2-selenouridine, we comparatively analyzed the oxidation reactions of sulfur-containing 2-thiouracil-5-carboxylic acid (s2c5Ura) and its selenium analog 2-selenouracil-5-carboxylic acid (se2c5Ura) using 1H-NMR spectroscopy, 77Se-NMR spectroscopy, and liquid chromatography-mass spectrometry. Treatment of s2c5Ura with hydrogen peroxide led to oxidized intermediates, followed by irreversible desulfurization to form uracil-5-carboxylic acid (c5Ura). In contrast, se2c5Ura oxidation resulted in a diselenide intermediate, followed by conversion to the seleninic acid, both of which could be readily reduced by ascorbate and glutathione. Glutathione and ascorbate only minimally prevented desulfurization of s2c5Ura, whereas very little deselenization of se2c5Ura occurred in the presence of the same antioxidants. In addition, se2c5Ura but not s2c5Ura showed glutathione peroxidase activity, further suggesting that oxidation of se2c5Ura is readily reversible, while oxidation of s2c5Ura is not. The results of the study of these model nucleobases suggest that the use of 2-selenouridine is related to resistance to oxidative inactivation that otherwise characterizes 2-thiouridine. As the use of selenocysteine in proteins also confers resistance to oxidation, our findings suggest a

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).

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}.

Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability.

Science.gov (United States)

Morton, B R

1993-09-01

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

In vivo induction of 4-thiouridine-cytidine adducts in tRNA of E. coli B/r by near-ultraviolet radiation

International Nuclear Information System (INIS)

Ramabhadran, T.V.; Fossum, T.; Jagger, J.

1976-01-01

Near-ultraviolet (near-UV; 320 to 405 nm) irradiation of Escherichia coli B/r induced the formation in vivo of 4 Srd-Cyd adducts in transfer RNA, as evidenced by (1) fluorescence spectrum changes of tRNA extracted from irradiated cells and reduced with NaBH 4 , (2) thin-layer chromatography on cellulose of hydrolysates of trichloroacetic acid-precipitable extracts of irradiated cells, and (3) comparison of these findings with adduct formation induced by near-UV irradiation of purified mixed tRNA from E.coli. The kinetics of induction of the 4 Srd-Cyd adduct in vivo, and the near-UV fluences required, provided strong support for our earlier hypothesis that formation of these adducts was responsible for near-UV-induced growth delay in E.coli. (author)

Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: Involvement of viral RNA sequences and the reverse transcriptase enzyme

NARCIS (Netherlands)

Abbink, Truus E. M.; Beerens, Nancy; Berkhout, Ben

2004-01-01

Human immunodeficiency virus type 1 uses the tRNA(3)(Lys) molecule as a selective primer for reverse transcription. This primer specificity is imposed by sequence complementarity between the tRNA primer and two motifs in the viral RNA genome: the primer-binding site (PBS) and the primer activation

Transcriptional Response of Selenopolypeptide Genes and Selenocysteine Biosynthesis Machinery Genes in Escherichia coli during Selenite Reduction.

Science.gov (United States)

Tetteh, Antonia Y; Sun, Katherine H; Hung, Chiu-Yueh; Kittur, Farooqahmed S; Ibeanu, Gordon C; Williams, Daniel; Xie, Jiahua

2014-01-01

Bacteria can reduce toxic selenite into less toxic, elemental selenium (Se(0)), but the mechanism on how bacterial cells reduce selenite at molecular level is still not clear. We used Escherichia coli strain K12, a common bacterial strain, as a model to study its growth response to sodium selenite (Na2SeO3) treatment and then used quantitative real-time PCR (qRT-PCR) to quantify transcript levels of three E. coli selenopolypeptide genes and a set of machinery genes for selenocysteine (SeCys) biosynthesis and incorporation into polypeptides, whose involvements in the selenite reduction are largely unknown. We determined that 5 mM Na2SeO3 treatment inhibited growth by ∼ 50% while 0.001 to 0.01 mM treatments stimulated cell growth by ∼ 30%. Under 50% inhibitory or 30% stimulatory Na2SeO3 concentration, selenopolypeptide genes (fdnG, fdoG, and fdhF) whose products require SeCys but not SeCys biosynthesis machinery genes were found to be induced ≥2-fold. In addition, one sulfur (S) metabolic gene iscS and two previously reported selenite-responsive genes sodA and gutS were also induced ≥2-fold under 50% inhibitory concentration. Our findings provide insight about the detoxification of selenite in E. coli via induction of these genes involved in the selenite reduction process.

Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein

Czech Academy of Sciences Publication Activity Database

Paris, Zdeněk; RUBIO, M. A. T.; Lukeš, Julius; Alfonzo, J. D.

2009-01-01

Roč. 15, č. 7 (2009), s. 1398-1406 ISSN 1355-8382 R&D Projects: GA ČR GA204/06/1558; GA MŠk LC07032; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : T. brucei * tRNA import * 2-thiolation * RIC * Rieske * Fe-S cluster Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.198, year: 2009

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

The structure of the hypothetical protein smu.1377c from Streptococcus mutans suggests a role in tRNA modification

International Nuclear Information System (INIS)

Fu, Tian-Min; Liu, Xiang; Li, Lanfen; Su, Xiao-Dong

2010-01-01

The crystal structure of smu.1377c, a hypothetical protein from S. mutans, shows a similar fold to Sua5-YciO-YrdC-family proteins and indicates its functional role in tRNA modification. Members of the Sua5-YciO-YrdC protein family are found in both eukaryotes and prokaryotes and possess a conserved α/β twisted open-sheet fold. The Escherichia coli protein YrdC has been shown to be involved in modification of tRNA. The crystal structure of smu.1377c, a hypothetical protein from Streptococcus mutans, has been determined to 2.25 Å resolution. From structure analysis and comparison, it is shown that smu.1377c is a member of the Sua5-YciO-YrdC family and that it may play the same role as E. coli YrdC

Essential Non-Translational Functions of tRNA Synthetases

Science.gov (United States)

Guo, Min; Schimmel, Paul

2013-01-01

Nontranslational functions of vertebrate aminoacyl tRNA synthetases (aaRSs), which catalyze the production of aminoacyl-tRNAs for protein synthesis, have recently been discovered. While these new functions were thought to be ‘moonlighting activities’, many are as critical for cellular homeostasis as the activity in translation. New roles have been associated with cytoplasmic forms as well as with nuclear and secreted extracellular forms that impact pathways for cardiovascular development, the immune response, and mTOR, IFN-γ and p53 signaling. The associations of aaRSs with autoimmune disorders, cancers and neurological disorders further highlight nontranslational functions of these proteins. Novel architecture elaborations of the aaRSs accompany their functional expansion in higher organisms and have been associated with the nontranslational functions for several aaRSs. While a general understanding of how these functions developed is limited, the expropriation of aaRSs for essential nontranslational functions may have been initiated by co-opting the amino acid binding site for another purpose. PMID:23416400

In vivo induction of 4-thiouridine-cytidine adducts in tRNA of E. coli B/r by near-ultraviolet radiation

Energy Technology Data Exchange (ETDEWEB)

Ramabhadran, T V; Fossum, T; Jagger, J [Texas Univ., Dallas (USA)

1976-05-01

Near-ultraviolet (near-UV; 320 to 405 nm) irradiation of Escherichia coli B/r induced the formation in vivo of /sup 4/Srd-Cyd adducts in transfer RNA, as evidenced by (1) fluorescence spectrum changes of tRNA extracted from irradiated cells and reduced with NaBH/sub 4/, (2) thin-layer chromatography on cellulose of hydrolysates of trichloroacetic acid-precipitable extracts of irradiated cells, and (3) comparison of these findings with adduct formation induced by near-UV irradiation of purified mixed tRNA from E.coli. The kinetics of induction of the /sup 4/Srd-Cyd adduct in vivo, and the near-UV fluences required, provided strong support for our earlier hypothesis that formation of these adducts was responsible for near-UV-induced growth delay in E.coli.

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......, respectively, in these three groups. The results indicate that RC enzyme analysis in muscle is not a sensitive test for MM in adults. In these patients, abnormal muscle histochemistry appears to be a better predictor ofMM....

Selenoproteins are essential for proper keratinocyte function and skin development.

Directory of Open Access Journals (Sweden)

Aniruddha Sengupta

2010-08-01

Full Text Available Dietary selenium is known to protect skin against UV-induced damage and cancer and its topical application improves skin surface parameters in humans, while selenium deficiency compromises protective antioxidant enzymes in skin. Furthermore, skin and hair abnormalities in humans and rodents may be caused by selenium deficiency, which are overcome by dietary selenium supplementation. Most important biological functions of selenium are attributed to selenoproteins, proteins containing selenium in the form of the amino acid, selenocysteine (Sec. Sec insertion into proteins depends on Sec tRNA; thus, knocking out the Sec tRNA gene (Trsp ablates selenoprotein expression. We generated mice with targeted removal of selenoproteins in keratin 14 (K14 expressing cells and their differentiated descendents. The knockout progeny had a runt phenotype, developed skin abnormalities and experienced premature death. Lack of selenoproteins in epidermal cells led to the development of hyperplastic epidermis and aberrant hair follicle morphogenesis, accompanied by progressive alopecia after birth. Further analyses revealed that selenoproteins are essential antioxidants in skin and unveiled their role in keratinocyte growth and viability. This study links severe selenoprotein deficiency to abnormalities in skin and hair and provides genetic evidence for the role of these proteins in keratinocyte function and cutaneous development.

Mutations in Cytosine-5 tRNA Methyltransferases Impact Mobile Element Expression and Genome Stability at Specific DNA Repeats

Directory of Open Access Journals (Sweden)

Bianca Genenncher

2018-02-01

Full Text Available The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5 RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects. In contrast, NSun2 function affected mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicated that tRNA-dependent processes affected mobile element expression and DNA repeat stability. Importantly, further experiments indicated that complex formation with RNA could also contribute to the impact of RCMT function on gene expression control. These results thus uncover a link between tRNA modification enzymes, the expression of repeat DNA, and genomic integrity.

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.

Transcriptional Response of Selenopolypeptide Genes and Selenocysteine Biosynthesis Machinery Genes in Escherichia coli during Selenite Reduction

Directory of Open Access Journals (Sweden)

Antonia Y. Tetteh

2014-01-01

Full Text Available Bacteria can reduce toxic selenite into less toxic, elemental selenium (Se0, but the mechanism on how bacterial cells reduce selenite at molecular level is still not clear. We used Escherichia coli strain K12, a common bacterial strain, as a model to study its growth response to sodium selenite (Na2SeO3 treatment and then used quantitative real-time PCR (qRT-PCR to quantify transcript levels of three E. coli selenopolypeptide genes and a set of machinery genes for selenocysteine (SeCys biosynthesis and incorporation into polypeptides, whose involvements in the selenite reduction are largely unknown. We determined that 5 mM Na2SeO3 treatment inhibited growth by ∼50% while 0.001 to 0.01 mM treatments stimulated cell growth by ∼30%. Under 50% inhibitory or 30% stimulatory Na2SeO3 concentration, selenopolypeptide genes (fdnG, fdoG, and fdhF whose products require SeCys but not SeCys biosynthesis machinery genes were found to be induced ≥2-fold. In addition, one sulfur (S metabolic gene iscS and two previously reported selenite-responsive genes sodA and gutS were also induced ≥2-fold under 50% inhibitory concentration. Our findings provide insight about the detoxification of selenite in E. coli via induction of these genes involved in the selenite reduction process.

Simulating movement of tRNA through the ribosome during hybrid-state formation.

Science.gov (United States)

Whitford, Paul C; Sanbonmatsu, Karissa Y

2013-09-28

Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function. A large biomolecular complex for which atomic models are available is the ribosome. In the cell, the ribosome reads messenger RNA (mRNA) in order to synthesize proteins. During this essential process, the ribosome undergoes a wide range of conformational rearrangements. One of the most poorly understood transitions is translocation: the process by which transfer RNA (tRNA) molecules move between binding sites inside of the ribosome. The first step of translocation is the adoption of a "hybrid" configuration by the tRNAs, which is accompanied by large-scale rotations in the ribosomal subunits. To illuminate the relationship between these rearrangements, we apply MD simulations using a multi-basin structure-based (SMOG) model, together with targeted molecular dynamics protocols. From 120 simulated transitions, we demonstrate the viability of a particular route during P/E hybrid-state formation, where there is asynchronous movement along rotation and tRNA coordinates. These simulations not only suggest an ordering of events, but they highlight atomic interactions that may influence the kinetics of hybrid-state formation. From these simulations, we also identify steric features (H74 and surrounding residues) encountered during the hybrid transition, and observe that flexibility of the single-stranded 3'-CCA tail is essential for it to reach the endpoint. Together, these simulations provide a set of structural and energetic signatures that suggest strategies for modulating the physical-chemical properties of protein synthesis by the

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 (Cornelia); 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

Crystallization and preliminary X-ray crystallographic characterization of TrmFO, a folate-dependent tRNA methyltransferase from Thermotoga maritima

International Nuclear Information System (INIS)

Cicmil, Nenad

2008-01-01

T. maritima TrmFO was overexpressed, purified and crystallized. A diffraction data set was collected to a resolution of 2.6 Å. TrmFO, previously classified as GID, is a methyltransferase that catalyzes the formation of 5-methyluridine or ribothymidine (T) at position 54 in tRNA in some Gram-positive bacteria. To date, TrmFO is the only characterized tRNA methyltransferase that does not use S-adenosylmethionine as the methyl-group donor. Instead, the donor of the methyl group is N 5 ,N 10 -methylenetetrahydrofolate. The crystallization and preliminary X-ray crystallographic studies of TrmFO are reported here. The recombinant protein, cloned from Thermotoga maritima genomic DNA, was overproduced in Esherichia coli and crystallized in 25%(v/v) PEG 4000, 100 mM NaCl and sodium citrate buffer pH 5.0 at 291 K using the hanging-drop vapor-diffusion method. The plate-shaped crystals diffracted to 2.6 Å and belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 79.94, b = 92.46, c = 127.20 Å

Hydrogen bond indices and tertiary structure of yeast tRNA sup(Phe)

International Nuclear Information System (INIS)

Giambiagi, M.S. de; Giambiagi, M.; Esquivel, D.M.S.

1982-01-01

The rigidity and stability of the tertiary structure of yeast tRNA sup(Phe) is related to a bond index employed in an IEHT calculation. The index permits a quantitative estimate of the electronic cloud along the hydrogen bond, having thus an appealing physical meaning. The results indicate that Hoogsteen-type bonds have, as expected, greater electronic population than Watson-Crick type ones. Other non-Watson-Crick pairings, the wobble pair and G 15 -C 48 , exhibit high values of the index for the NH...O bond. In the triples, the electronic density of the hydrogen bridges does not weaken, comparing it with the one of the pairs involved. Contour density maps are shown and dipolar moments of pairs and triples are qualitatively discussed. (Author) [pt

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.

Crystallization and preliminary X-ray crystallographic characterization of TrmFO, a folate-dependent tRNA methyltransferase from Thermotoga maritima

Energy Technology Data Exchange (ETDEWEB)

Cicmil, Nenad, E-mail: cicmil@uiuc.edu [Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2008-03-01

T. maritima TrmFO was overexpressed, purified and crystallized. A diffraction data set was collected to a resolution of 2.6 Å. TrmFO, previously classified as GID, is a methyltransferase that catalyzes the formation of 5-methyluridine or ribothymidine (T) at position 54 in tRNA in some Gram-positive bacteria. To date, TrmFO is the only characterized tRNA methyltransferase that does not use S-adenosylmethionine as the methyl-group donor. Instead, the donor of the methyl group is N{sup 5},N{sup 10}-methylenetetrahydrofolate. The crystallization and preliminary X-ray crystallographic studies of TrmFO are reported here. The recombinant protein, cloned from Thermotoga maritima genomic DNA, was overproduced in Esherichia coli and crystallized in 25%(v/v) PEG 4000, 100 mM NaCl and sodium citrate buffer pH 5.0 at 291 K using the hanging-drop vapor-diffusion method. The plate-shaped crystals diffracted to 2.6 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 79.94, b = 92.46, c = 127.20 Å.

The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA

Science.gov (United States)

Chatterjee, Kunal; Blaby, Ian K.; Thiaville, Patrick C.; Majumder, Mrinmoyee; Grosjean, Henri; Yuan, Y. Adam; Gupta, Ramesh; de Crécy-Lagard, Valérie

2012-01-01

The methylation of pseudouridine (Ψ) at position 54 of tRNA, producing m1Ψ, is a hallmark of many archaeal species, but the specific methylase involved in the formation of this modification had yet to be characterized. A comparative genomics analysis had previously identified COG1901 (DUF358), part of the SPOUT superfamily, as a candidate for this missing methylase family. To test this prediction, the COG1901 encoding gene, HVO_1989, was deleted from the Haloferax volcanii genome. Analyses of modified base contents indicated that while m1Ψ was present in tRNA extracted from the wild-type strain, it was absent from tRNA extracted from the mutant strain. Expression of the gene encoding COG1901 from Halobacterium sp. NRC-1, VNG1980C, complemented the m1Ψ minus phenotype of the ΔHVO_1989 strain. This in vivo validation was extended with in vitro tests. Using the COG1901 recombinant enzyme from Methanocaldococcus jannaschii (Mj1640), purified enzyme Pus10 from M. jannaschii and full-size tRNA transcripts or TΨ-arm (17-mer) fragments as substrates, the sequential pathway of m1Ψ54 formation in Archaea was reconstituted. The methylation reaction is AdoMet dependent. The efficiency of the methylase reaction depended on the identity of the residue at position 55 of the TΨ-loop. The presence of Ψ55 allowed the efficient conversion of Ψ54 to m1Ψ54, whereas in the presence of C55, the reaction was rather inefficient and no methylation reaction occurred if a purine was present at this position. These results led to renaming the Archaeal COG1901 members as TrmY proteins. PMID:22274953

A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Science.gov (United States)

Zaborske, John M; DuMont, Vanessa L Bauer; Wallace, Edward W J; Pan, Tao; Aquadro, Charles F; Drummond, D Allan

2014-12-01

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.

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.

Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling

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Viktor Scheidt

2014-11-01

Full Text Available Previous work in yeast has suggested that modification of tRNAs, in particular uridine bases in the anticodon wobble position (U34, is linked to TOR (target of rapamycin signaling. Hence, U34 modification mutants were found to be hypersensitive to TOR inhibition by rapamycin. To study whether this involves inappropriate TOR signaling, we examined interaction between mutations in TOR pathway genes (tip41∆, sap190∆, ppm1∆, rrd1∆ and U34 modification defects (elp3∆, kti12∆, urm1∆, ncs2∆ and found the rapamycin hypersensitivity in the latter is epistatic to drug resistance of the former. Epistasis, however, is abolished in tandem with a gln3∆ deletion, which inactivates transcription factor Gln3 required for TOR-sensitive activation of NCR (nitrogen catabolite repression genes. In line with nuclear import of Gln3 being under control of TOR and dephosphorylation by the Sit4 phosphatase, we identify novel TOR-sensitive sit4 mutations that confer rapamycin resistance and importantly, mislocalise Gln3 when TOR is inhibited. This is similar to gln3∆ cells, which abolish the rapamycin hypersensitivity of U34 modification mutants, and suggests TOR deregulation due to tRNA undermodification operates through Gln3. In line with this, loss of U34 modifications (elp3∆, urm1∆ enhances nuclear import of and NCR gene activation (MEP2, GAP1 by Gln3 when TOR activity is low. Strikingly, this stimulatory effect onto Gln3 is suppressed by overexpression of tRNAs that usually carry the U34 modifications. Collectively, our data suggest that proper TOR signaling requires intact tRNA modifications and that loss of U34 modifications impinges on the TOR-sensitive NCR branch via Gln3 misregulation.

Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling.

Science.gov (United States)

Scheidt, Viktor; Jüdes, André; Bär, Christian; Klassen, Roland; Schaffrath, Raffael

2014-11-29

Previous work in yeast has suggested that modification of tRNAs, in particular uridine bases in the anticodon wobble position (U34), is linked to TOR (target of rapamycin) signaling. Hence, U34 modification mutants were found to be hypersensitive to TOR inhibition by rapamycin. To study whether this involves inappropriate TOR signaling, we examined interaction between mutations in TOR pathway genes ( tip41 ∆, sap190 ∆, ppm1 ∆, rrd1 ∆) and U34 modification defects ( elp3 ∆, kti 12∆, urm1 ∆, ncs2 ∆) and found the rapamycin hypersensitivity in the latter is epistatic to drug resistance of the former. Epistasis, however, is abolished in tandem with a gln3 ∆ deletion, which inactivates transcription factor Gln3 required for TOR-sensitive activation of NCR (nitrogen catabolite repression) genes. In line with nuclear import of Gln3 being under control of TOR and dephosphorylation by the Sit4 phosphatase, we identify novel TOR-sensitive sit4 mutations that confer rapamycin resistance and importantly, mislocalise Gln3 when TOR is inhibited. This is similar to gln3 ∆ cells, which abolish the rapamycin hypersensitivity of U34 modification mutants, and suggests TOR deregulation due to tRNA undermodification operates through Gln3. In line with this, loss of U34 modifications ( elp3 ∆, urm1 ∆) enhances nuclear import of and NCR gene activation ( MEP2 , GAP1 ) by Gln3 when TOR activity is low. Strikingly, this stimulatory effect onto Gln3 is suppressed by overexpression of tRNAs that usually carry the U34 modifications. Collectively, our data suggest that proper TOR signaling requires intact tRNA modifications and that loss of U34 modifications impinges on the TOR-sensitive NCR branch via Gln3 misregulation.

In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

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Czudnochowski, Nadine; Wang, Amy Liya; Finer-Moore, Janet; Stroud, Robert M

2013-10-23

Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

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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.

The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications.

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Dewe, Joshua M; Whipple, Joseph M; Chernyakov, Irina; Jaramillo, Laura N; Phizicky, Eric M

2012-10-01

The structural and functional integrity of tRNA is crucial for translation. In the yeast Saccharomyces cerevisiae, certain aberrant pre-tRNA species are subject to nuclear surveillance, leading to 3' exonucleolytic degradation, and certain mature tRNA species are subject to rapid tRNA decay (RTD) if they are appropriately hypomodified or bear specific destabilizing mutations, leading to 5'-3' exonucleolytic degradation by Rat1 and Xrn1. Thus, trm8-Δ trm4-Δ strains are temperature sensitive due to lack of m(7)G(46) and m(5)C and the consequent RTD of tRNA(Val(AAC)), and tan1-Δ trm44-Δ strains are temperature sensitive due to lack of ac(4)C(12) and Um(44) and the consequent RTD of tRNA(Ser(CGA)) and tRNA(Ser(UGA)). It is unknown how the RTD pathway interacts with translation and other cellular processes, and how generally this pathway acts on hypomodified tRNAs. We provide evidence here that elongation factor 1A (EF-1A) competes with the RTD pathway for substrate tRNAs, since its overexpression suppresses the tRNA degradation and the growth defect of strains subject to RTD, whereas reduced levels of EF-1A have the opposite effect. We also provide evidence that RTD acts on a variety of tRNAs lacking one or more different modifications, since trm1-Δ trm4-Δ mutants are subject to RTD of tRNA(Ser(CGA)) and tRNA(Ser(UGA)) due to lack of m(2,2)G(26) and m(5)C, and since trm8-Δ, tan1-Δ, and trm1-Δ single mutants are each subject to RTD. These results demonstrate that RTD interacts with the translation machinery and acts widely on hypomodified tRNAs.

Selenoproteins-What unique properties can arise with selenocysteine in place of cysteine?

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Arnér, Elias S J

2010-05-01

The defining entity of a selenoprotein is the inclusion of at least one selenocysteine (Sec) residue in its sequence. Sec, the 21st naturally occurring genetically encoded amino acid, differs from its significantly more common structural analog cysteine (Cys) by the identity of a single atom: Sec contains selenium instead of the sulfur found in Cys. Selenium clearly has unique chemical properties that differ from sulfur, but more striking are perhaps the similarities between the two elements. Selenium was discovered by Jöns Jacob Berzelius, a renowned Swedish scientist instrumental in establishing the institution that would become Karolinska Institutet. Written at the occasion of the bicentennial anniversary of Karolinska Institutet, this mini review focuses on the unique selenium-derived properties that may potentially arise in a protein upon the inclusion of Sec in place of Cys. With 25 human genes encoding selenoproteins and in total several thousand selenoproteins yet described in nature, it seems likely that the presence of that single selenium atom of Sec should convey some specific feature, thereby explaining the existence of selenoproteins in spite of demanding and energetically costly Sec-specific synthesis machineries. Nonetheless, most, if not all, of the currently known selenoproteins are also found as Cys-containing non-selenoprotein orthologues in other organisms, wherefore any potentially unique properties of selenoproteins are yet a matter of debate. The pK(a) of free Sec (approximately 5.2) being significantly lower than that of free Cys (approximately 8.5) has often been proposed as one of the unique features of Sec. However, as discussed herein, this pK(a) difference between Sec and Cys can hardly provide an evolutionary pressure for maintenance of selenoproteins. Moreover, the typically 10- to 100-fold lower enzymatic efficiencies of Sec-to-Cys mutants of selenoprotein oxidoreductases, are also weak arguments for the overall existence of

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

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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.

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

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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.

Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative.

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Hountondji, Codjo; Créchet, Jean-Bernard; Le Caër, Jean-Pierre; Lancelot, Véronique; Cognet, Jean A H; Baouz, Soria

2017-12-01

In this report, we have used periodate-oxidized tRNA (tRNAox) as an affinity laleling reagent to demonstrate that: (i) the bL12 protein contacts the CCA-arm of P-site bound tRNA on the Escherichia coli 70S ribosomes; (ii) the stoichiometry of labelling is one molecule of tRNAox bound to one polypeptide chain of endogenous bL12; (iii) cross-linking in situ of bL12 with tRNAox on the ribosomes provokes the loss of activity; (iv) intact tRNA protects bL12 in the 70S ribosomes against cross-linking with tRNAox; (v) both tRNAox and pyridoxal 5'-phosphate (PLP) compete for the same or for proximal cross-linking site(s) on bL12 inside the ribosome; (vi) the stoichiometry of cross-linking of PLP to the recombinant E. coli bL12 protein is one molecule of PLP covalently bound per polypeptide chain; (vii) the amino acid residue of recombinant bL12 cross-linked with PLP is Lys-65; (viii) Lys-65 of E. coli bL12 corresponds to Lys-53 of eL42 which was previously shown to cross-link with P-site bound tRNAox on human 80S ribosomes in situ; (ix) finally, E. coli bL12 and human eL42 proteins display significant primary structure similarities, which argues for evolutionary conservation of these two proteins located at the tRNA-CCA binding site on eubacterial and eukaryal ribosomes. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

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

International Nuclear Information System (INIS)

Ciesiolka, J.; Nurse, K.; Klein, J.; Ofengand, J.

1985-01-01

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

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

The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH......1-8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity...... was previously demonstrated for one such protein. To further explore this apparent functional duality of the ALKBH8 proteins, we have here enzymatically characterized a panel of such proteins, originating from bacteria, protozoa and mimivirus. All the enzymes showed DNA repair activity in vitro, but...

Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing.

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Jones, Christopher P; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

2013-02-01

The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.

Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation.

Science.gov (United States)

Rayevsky, A V; Sharifi, M; Tukalo, M A

2017-09-01

Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA Leu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA Leu and isoleucyl-tRNA Leu . In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS. Copyright © 2017 Elsevier Inc. All rights reserved.

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

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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.

Quasi-adequate semigroups

International Nuclear Information System (INIS)

El-Qallali, A.

1987-11-01

The least fundamental adequate good congruence on an arbitrary type W semigroup S is described as well as the largest superabundant full subsemigroup of S and the largest full subsemigroup of S which is a band of cancellative monoids. Weak type W semigroups are defined by replacing the idempotent-connected property in type W by one of its consequences and a structure theorem is obtained for such semigroups. (author). 12 refs

Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

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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.

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

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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.

Adequate supervision for children and adolescents.

Science.gov (United States)

Anderst, James; Moffatt, Mary

2014-11-01

Primary care providers (PCPs) have the opportunity to improve child health and well-being by addressing supervision issues before an injury or exposure has occurred and/or after an injury or exposure has occurred. Appropriate anticipatory guidance on supervision at well-child visits can improve supervision of children, and may prevent future harm. Adequate supervision varies based on the child's development and maturity, and the risks in the child's environment. Consideration should be given to issues as wide ranging as swimming pools, falls, dating violence, and social media. By considering the likelihood of harm and the severity of the potential harm, caregivers may provide adequate supervision by minimizing risks to the child while still allowing the child to take "small" risks as needed for healthy development. Caregivers should initially focus on direct (visual, auditory, and proximity) supervision of the young child. Gradually, supervision needs to be adjusted as the child develops, emphasizing a safe environment and safe social interactions, with graduated independence. PCPs may foster adequate supervision by providing concrete guidance to caregivers. In addition to preventing injury, supervision includes fostering a safe, stable, and nurturing relationship with every child. PCPs should be familiar with age/developmentally based supervision risks, adequate supervision based on those risks, characteristics of neglectful supervision based on age/development, and ways to encourage appropriate supervision throughout childhood. Copyright 2014, SLACK Incorporated.

Funding an 'Adequate' Education.

Science.gov (United States)

Guthrie, James W.

1983-01-01

The U.S. political process has been used to define an "adequate" education, in terms of resources, procedures, content, or outcomes. The marketplace also allows individuals to define adequacy through various voucher arrangements. Both mechanisms should be used, based on whether public or private interests are paramount in a particular…

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

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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.

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... ACT HEALTH AND SAFETY DATA REPORTING General Provisions § 716.25 Adequate file search. The scope of a person's responsibility to search records is limited to records in the location(s) where the required...

Sequence organization and control of transcription in the bacteriophage T4 tRNA region.

Science.gov (United States)

Broida, J; Abelson, J

1985-10-05

Bacteriophage T4 contains genes for eight transfer RNAs and two stable RNAs of unknown function. These are found in two clusters at 70 X 10(3) base-pairs on the T4 genetic map. To understand the control of transcription in this region we have completed the sequencing of 5000 base-pairs in this region. The sequence contains a part of gene 3, gene 1, gene 57, internal protein I, the tRNA genes and five open reading frames which most likely code for heretofore unidentified proteins. We have used subclones of the region to investigate the kinetics of transcription in vivo. The results show that transcription in this region consists of overlapping early, middle and late transcripts. Transcription is directed from two early promoters, one or two middle promoters and perhaps two late promoters. This region contains all of the features that are seen in T4 transcription and as such is a good place to study the phenomenon in more detail.

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 an...

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.

Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

Science.gov (United States)

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Hisashi Ishida

Full Text Available To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

Enrichment of African catfish with functional selenium originating from garlic

NARCIS (Netherlands)

Schram, E.; Pedrero, Z.; Camara, C.; Heul, van der J.W.; Luten, J.B.

2008-01-01

We wanted to create functional seafood with high concentrations of organic selenium (seleno-methyl-selenocysteine and ¿-glutamyl-seleno-methyl-selenocysteine) with anti-carcinogenic properties for human consumers. Garlic containing high concentrations of these organic selenium compounds was used as

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

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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.

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

Directory of Open Access Journals (Sweden)

Paul C Whitford

Full Text Available 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.

Perception of Mothers on Adequate Nutrition

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Darshini Valoo

2017-03-01

Full Text Available Background: Malnutrition in children less than 5 years old persists around the world. In West Java and one of the districts of West Java (Sumedang, the prevalence of malnutrition is about 18.5% and 15.8% respectively. Numerous factors can lead to child malnutrition. Difficulties in availability, accessibility, acceptability and quality of food can be contributing factors. A good perception of mother on adequate nutrition can improve children’s nutritional status. This study was conducted to study the perception of mothers with children 2 to 5 years old on adequate nutrition. Methods: Most of the respondents had good perception on the aspect of adequate nutrition. Results showed perception on availability was 83.8%, physical accessibility was 97.1%, economical accessibility was 98.6%, information accessibility was 84.8% and acceptability was 81.0%. However, perception of respondents on good quality nutrition for the main meal and additional food was still poor. Moreover, there are taboos for eating shrimp and watermelon. Additionally, children were given snacks in large amount. Results: There was a strong correlation between mid-upper arm muscle area/size and muscular strength (correlation cooefficient 0.746. Moreover, the higher the Body Mass Index, the stronger the muscle strength was to some point. If the BMI was more than 25 kg/m2, this findings did not occurred. Conclusions: This study reveals that the perception of mothers on good quality food is poor regardless the good results on availibility, accesibility and acceptability.

Kissing loops hide premature termination codons in pre-mRNAof selenoprotein genes and in genes containing programmedribosomal frameshifts

DEFF Research Database (Denmark)

Knudsen, Steen; Brunak, Søren

1997-01-01

A novel RNA secondary structure that places the selenocysteine codon UGA in one hairpin and a donor splice site in another, has been discovered in selenoprotein genes. The presence of the structure resolves the discrepancy that the selenocysteine triplet, UGA, should block splicing. Without a spe...

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 NMVC...

Selenium-containing enzymes in mammals: Chemical perspectives

Indian Academy of Sciences (India)

The role of selenocysteine moiety in natural mammalian enzymes such as glutathione peroxidase (GPx), iodothyronine deiodinase (ID) and thioredoxin reductase (TrxR) is highlighted and the effect of other amino acid residues located in close proximity to selenocysteine is described. It is evident from various studies that ...

Selenium-containing enzymes in mammals: Chemical perspectives

Indian Academy of Sciences (India)

Unknown

Abstract. The chemical and biochemical route to the synthesis of the 21st amino acid in living systems, selenocysteine, is described. The incorporation of this rare amino acid residue into proteins is described with emphasis on the role of monoselenophosphate as selenium source. The role of selenocysteine moiety in.

Cardiac abnormalities in diabetic patients with mutation in the mitochondrial tRNA Leu(UUR)Gene

International Nuclear Information System (INIS)

Ueno, Hiroshi; Shiotani, Hideyuki

1999-01-01

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 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 0.05). 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 Leu(UUR) gene. (author)

Iron absorption from adequate Filipinos meals

International Nuclear Information System (INIS)

Trinidad, T.P.; Madriaga, J.R.; Valdez, D.H.; Cruz, E.M.; Mallillin, A.C.; Sison, C.C.; Kuizon, M.D.

1989-01-01

Iron absorption from adequate Filipino meals representing the three major island groups of the Philippines (Luzon, Visayas, and Mindanao) was studied using double isotope extrinsic tag method. Mean iron absorption of the one-day meal for Metro Manila was 6.6 +- 1.26%. Central Visayas, 6.3 +- 1.15% and Southern Mindanao, 6.4 +- 1.19%. Comparison between meals (breakfast, lunch, dinner) for each region as well as one-day meal for the three regions showed no significant differences (P>0.01). Correlation tests done between iron absorption and the following iron enhancers: ascorbic acid, amount of fish, meat or poultry; and inhibitors: phytic acid and tannic acid, did not give significant results. The overall average of 6.4 +- 1.20% may be used as the iron absorption level from an adequate Filipino meal. This value can be considered as one of the bases for arriving at recommended dietary allowances for iron among Filipinos instead of the 10% iron absorption assumed in 1976. (Auth.). 21 refs.; 3 tabs.; 3 annexes

Iron absorption from adequate Filipino meals

International Nuclear Information System (INIS)

Trinidad, T.P.; Madriaga, J.R.; Valdez, D.H.; Cruz, E.M.; Mallillin, A.C.; Sison, C.C.; Kuizon, M.D.

1991-01-01

Iron absorption from adequate Filipino meals representing the three major island groups of the Philippines (Luzon, Visayas and Mindanao) was studied using double isotope extrinsic tag method. Mean iron absorption of the one-day meal for Metro Manila was 6.6 ± 1.26%, Central Visayas, 6.3 ± 1.15% and Southern Mindanao, 6.4 ± 1.19%. Comparison between meals (breakfast, lunch, dinner) for each region as well as one-day meal for the three regions showed no significant differences (P > .01). Correlation tests done between iron absorption and the following iron enhancers: ascorbic acid, amount of fish, meat or poultry and inhibitors: phytic acid and tannic acid did not give significant results. The overall bar x of 6.4 ± 1.20% may be used as the non-heme iron absorption level from an adequate Filipino meal. This value can be considered as one of the bases for arriving at recommended dietary allowances for iron among Filipinos instead of the 10% iron absorption assumed in 1976

9 CFR 2.33 - Attending veterinarian and adequate veterinary care.

Science.gov (United States)

2010-01-01

... veterinary care. 2.33 Section 2.33 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE... 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...

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

Science.gov (United States)

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-01

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Arabidopsis: an adequate model for dicot root systems?

Directory of Open Access Journals (Sweden)

Richard W Zobel

2016-02-01

Full Text Available 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 these classes of root. This then suggests that Arabidopsis root research can be considered an adequate model for eudicot plant root systems.

Structure–function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

International Nuclear Information System (INIS)

Meineke, Birthe; Shuman, Stewart

2012-01-01

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.

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.

Towards an Integrative Understanding of tRNA Aminoacylation-Diet-Host-Gut Microbiome Interactions in Neurodegeneration.

Science.gov (United States)

Paley, Elena L; Perry, George

2018-03-26

Transgenic mice used for Alzheimer's disease (AD) preclinical experiments do not recapitulate the human disease. In our models, the dietary tryptophan metabolite tryptamine produced by human gut microbiome induces tryptophanyl-tRNA synthetase (TrpRS) deficiency with consequent neurodegeneration in cells and mice. Dietary supplements, antibiotics and certain drugs increase tryptamine content in vivo. TrpRS catalyzes tryptophan attachment to tRNA trp at initial step of protein biosynthesis. Tryptamine that easily crosses the blood-brain barrier induces vasculopathies, neurodegeneration and cell death via TrpRS competitive inhibition. TrpRS inhibitor tryptophanol produced by gut microbiome also induces neurodegeneration. TrpRS inhibition by tryptamine and its metabolites preventing tryptophan incorporation into proteins lead to protein biosynthesis impairment. Tryptophan, a least amino acid in food and proteins that cannot be synthesized by humans competes with frequent amino acids for the transport from blood to brain. Tryptophan is a vulnerable amino acid, which can be easily lost to protein biosynthesis. Some proteins marking neurodegenerative pathology, such as tau lack tryptophan. TrpRS exists in cytoplasmic (WARS) and mitochondrial (WARS2) forms. Pathogenic gene variants of both forms cause TrpRS deficiency with consequent intellectual and motor disabilities in humans. The diminished tryptophan-dependent protein biosynthesis in AD patients is a proof of our model-based disease concept.

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...... gene (LARS2), involved in aminoacylation of tRNA(Leu(UUR)), associate with type 2 diabetes. Direct sequencing of LARS2 cDNA from 25 type 2 diabetic subjects revealed eight single nucleotide polymorphisms. Two of the variants were examined in 7,836 subjects from four independent populations...... in the Netherlands and Denmark. A -109 g/a variant was not associated with type 2 diabetes. Allele frequencies for the other variant, H324Q, were 3.5% in type 2 diabetic and 2.7% in control subjects, respectively. The common odds ratio across all four studies was 1.40 (95% CI 1.12-1.76), P = 0.004. There were...

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

Selenoproteins in Archaea and Gram-positive bacteria.

Science.gov (United States)

Stock, Tilmann; Rother, Michael

2009-11-01

Selenium is an essential trace element for many organisms by serving important catalytic roles in the form of the 21st co-translationally inserted amino acid selenocysteine. It is mostly found in redox-active proteins in members of all three domains of life and analysis of the ever-increasing number of genome sequences has facilitated identification of the encoded selenoproteins. Available data from biochemical, sequence, and structure analyses indicate that Gram-positive bacteria synthesize and incorporate selenocysteine via the same pathway as enterobacteria. However, recent in vivo studies indicate that selenocysteine-decoding is much less stringent in Gram-positive bacteria than in Escherichia coli. For years, knowledge about the pathway of selenocysteine synthesis in Archaea and Eukarya was only fragmentary, but genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has not only led to the characterization of the pathways but has also shown that they are principally identical. This review summarizes current knowledge about the metabolic pathways of Archaea and Gram-positive bacteria where selenium is involved, about the known selenoproteins, and about the respective pathways employed in selenoprotein synthesis.

The Effectiveness of Clinician Education on the Adequate ...

African Journals Online (AJOL)

information to make their input in the patient's management.[1]. Some errors in ... to insufficient, and/or illegible clinical information provided ... Adequate Completion of Laboratory Test Request. Forms at a ..... the system prior to the posttest.

Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase

International Nuclear Information System (INIS)

Guo, Min; Shapiro, Ryan; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

E. coli alanyl-tRNA synthetase is recalcitrant to crystallization. A group of leucine substitutions has transformed the protein. Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an α-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered α-helix did not form a leucine zipper that interlocked with the same α-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Science.gov (United States)

Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

2018-01-01

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

Polycistronic tRNA and CRISPR guide-RNA enables highly efficient multiplexed genome engineering in human cells.

Science.gov (United States)

Dong, Fengping; Xie, Kabin; Chen, Yueying; Yang, Yinong; Mao, Yingwei

2017-01-22

CRISPR/Cas9 has been widely used for genomic editing in many organisms. Many human diseases are caused by multiple mutations. The CRISPR/Cas9 system provides a potential tool to introduce multiple mutations in a genome. To mimic complicated genomic variants in human diseases, such as multiple gene deletions or mutations, two or more small guide RNAs (sgRNAs) need to be introduced all together. This can be achieved by separate Pol III promoters in a construct. However, limited enzyme sites and increased insertion size lower the efficiency to make a construct. Here, we report a strategy to quickly assembly multiple sgRNAs in one construct using a polycistronic-tRNA-gRNA (PTG) strategy. Taking advantage of the endogenous tRNA processing system in mammalian cells, we efficiently express multiple sgRNAs driven using only one Pol III promoter. Using an all-in-one construct carrying PTG, we disrupt the deacetylase domain in multiple histone deacetylases (HDACs) in human cells simultaneously. We demonstrate that multiple HDAC deletions significantly affect the activation of the Wnt-signaling pathway. Thus, this method enables to efficiently target multiple genes and provide a useful tool to establish mutated cells mimicking human diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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...... 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...... activity of AtTRM9 depends on either one of two closely related proteins, AtTRM112a and AtTRM112b. Moreover, we demonstrate that AT1G36310, denoted AtALKBH8, is required for hydroxylation of mcm(5)U to (S)-mchm(5)U in tRNA(Gly)(UCC), and has a function similar to the mammalian dioxygenase ALKBH8...

Child malnutrition and mortality among families not utilizing adequately iodized salt in Indonesia.

Science.gov (United States)

Semba, Richard D; de Pee, Saskia; Hess, Sonja Y; Sun, Kai; Sari, Mayang; Bloem, Martin W

2008-02-01

Salt iodization is the main strategy for reducing iodine deficiency disorders worldwide. Characteristics of families not using iodized salt need to be known to expand coverage. The objective was to determine whether families who do not use iodized salt have a higher prevalence of child malnutrition and mortality and to identify factors associated with not using iodized salt. Use of adequately iodized salt (>or =30 ppm), measured by rapid test kits, was assessed between January 1999 and September 2003 in 145 522 and 445 546 families in urban slums and rural areas, respectively, in Indonesia. Adequately iodized salt was used by 66.6% and 67.2% of families from urban slums and rural areas, respectively. Among families who used adequately iodized salt, mortality in neonates, infants, and children aged urban slums; among families who did not use adequately iodized salt, the respective values were 4.2% compared with 6.3%, 7.1% compared with 11.2%, and 8.5% compared with 13.3% (P rural areas. Families not using adequately iodized salt were more likely to have children who were stunted, underweight, and wasted. In multivariate analyses that controlled for potential confounders, low maternal education was the strongest factor associated with not using adequately iodized salt. In Indonesia, nonuse of adequately iodized salt is associated with a higher prevalence of child malnutrition and mortality in neonates, infants, and children aged <5 y. Stronger efforts are needed to expand salt iodization in Indonesia.

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

NARCIS (Netherlands)

mr.dr. Bart F.W. Wernaart

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

Is the Marketing Concept Adequate for Continuing Education?

Science.gov (United States)

Rittenburg, Terri L.

1984-01-01

Because educators have a social responsibility to those they teach, the marketing concept may not be adequate as a philosophy for continuing education. In attempting to broaden the audience for continuing education, educators should consider a societal marketing concept to meet the needs of the educationally disadvantaged. (SK)

How adequate policies can push renewables

International Nuclear Information System (INIS)

Goldemberg, J.; Coelho, S.T.; Lucon, Oswaldo

2004-01-01

The growing interest in the establishment of a minimum share of renewable sources in the world energy matrix, after the Johannesburg's World Summit for Sustainable Development (WSSD), has raised the question about the means for such new technologies to compete with the traditional ones. The Brazilian experience in the last 25 years with ethanol as a replacement for gasoline can illustrate this possibility. Moreover, recent policies introduced by the Federal government for a minimum share of new renewable sources - wind, modern biomass and small hydro - in the Brazilian electricity matrix reinforces the country's commitment to utilize adequate policies for achieving sustainable development

Is prophetic discourse adequate to address global economic justice?

African Journals Online (AJOL)

Test

2011-02-15

Feb 15, 2011 ... of moral discourse adequately addresses issues of economic injustice. ... plays an indispensable role in addressing issues of global economic justice, but ...... governance in their business practices, to provide a tool for a.

Comparability and Reliability Considerations of Adequate Yearly Progress

Science.gov (United States)

Maier, Kimberly S.; Maiti, Tapabrata; Dass, Sarat C.; Lim, Chae Young

2012-01-01

The purpose of this study is to develop an estimate of Adequate Yearly Progress (AYP) that will allow for reliable and valid comparisons among student subgroups, schools, and districts. A shrinkage-type estimator of AYP using the Bayesian framework is described. Using simulated data, the performance of the Bayes estimator will be compared to…

Region 6: Texas Austin Adequate Letter (11/23/2016)

Science.gov (United States)

EPA letter approves the Motor Vehicle Emissions Budgets contained in the latest revision to Dallas/Fort Worth 2008 8-hour Ozone State Implementation Plan, finding them adequate for transportation conformity purposes to be announced in the Federal Register.

Study Concerning Exercising an Adequate Professional Reasoning in Developing the Evaluation and Audit

Directory of Open Access Journals (Sweden)

Vârteiu Daniel Petru

2017-01-01

Even though there are regulations which clearly specify the way in which an evaluation process, respectively an adequate audit process must take place, for a good management of encountered situations and difficulties, the evaluator, respectively the auditor must exercise an adequate professional reasoning.

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... and Adequate Veterinary Care § 2.40 Attending veterinarian and adequate veterinary care (dealers and... veterinary care to its animals in compliance with this section. (1) Each dealer and exhibitor shall employ an...

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

Characterization of mitochondrial thioredoxin reductase from C. elegans

International Nuclear Information System (INIS)

Lacey, Brian M.; Hondal, Robert J.

2006-01-01

Thioredoxin reductase catalyzes the NADPH-dependent reduction of the catalytic disulfide bond of thioredoxin. In mammals and other higher eukaryotes, thioredoxin reductases contain the rare amino acid selenocysteine at the active site. The mitochondrial enzyme from Caenorhabditis elegans, however, contains a cysteine residue in place of selenocysteine. The mitochondrial C. elegans thioredoxin reductase was cloned from an expressed sequence tag and then produced in Escherichia coli as an intein-fusion protein. The purified recombinant enzyme has a k cat of 610 min -1 and a K m of 610 μM using E. coli thioredoxin as substrate. The reported k cat is 25% of the k cat of the mammalian enzyme and is 43-fold higher than a cysteine mutant of mammalian thioredoxin reductase. The enzyme would reduce selenocysteine, but not hydrogen peroxide or insulin. The flanking glycine residues of the GCCG motif were mutated to serine. The mutants improved substrate binding, but decreased the catalytic rate

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... the security and privacy of such records. (5) The disposal and destruction of identifiable personal....14 Section 200.14 Accounts RECOVERY ACCOUNTABILITY AND TRANSPARENCY BOARD PRIVACY ACT OF 1974 § 200...

An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

Science.gov (United States)

Iwasaki, Yuki; Abe, Takashi; Wada, Kennosuke; Wada, Yoshiko; Ikemura, Toshimichi

2017-09-12

Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions. This unsupervised clustering can reveal combinatorial oligonucleotide motifs that are responsible for the amino acid-dependent clustering, as well as other functionally and structurally important consensus motifs, which have been evolutionarily conserved. BLSOM is also useful for identifying tDNAs as phylogenetic markers for special phylotypes. When we constructed BLSOM with 'species-unknown' tDNAs from metagenomic sequences plus 'species-known' microbial tDNAs, a large portion of metagenomic tDNAs self-organized with species-known tDNAs, yielding information on microbial communities in environmental samples. BLSOM can also enhance accuracy in the tDNA database obtained from big sequence data. This unsupervised data mining should become important for studying numerous functionally unclear RNAs obtained from a wide range of organisms.

Is prophetic discourse adequate to address global economic justice?

Directory of Open Access Journals (Sweden)

Piet J. Naudé

2011-04-01

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.

Cognitive Attributes of Adequate and Inadequate Responders to Reading Intervention in Middle School

Science.gov (United States)

Miciak, Jeremy; Stuebing, Karla K.; Vaughn, Sharon; Roberts, Greg; Barth, Amy E.; Fletcher, Jack M.

2014-01-01

No studies have investigated the cognitive attributes of middle school students who are adequate and inadequate responders to Tier 2 reading intervention. We compared students in Grades 6 and 7 representing groups of adequate responders (n = 77) and inadequate responders who fell below criteria in (a) comprehension (n = 54); (b) fluency (n = 45);…

Yeast tRNAPhe expressed in human cells can be selected by HIV-1 for use as a reverse transcription primer

International Nuclear Information System (INIS)

Kelly, Nathan J.; Morrow, Casey D.

2003-01-01

All naturally occurring human immune deficiency viruses (HIV-1) select and use tRNA Lys,3 as the primer for reverse transcription. Studies to elucidate the mechanism of tRNA selection from the intracellular milieu have been hampered due to the difficulties in manipulating the endogenous levels of tRNA Lys,3 . We have previously described a mutant HIV-1 with a primer binding site (PBS) complementary to yeast tRNA Phe (psHIV-Phe) that relies on transfection of yeast tRNA Phe for infectivity. To more accurately recapitulate the selection process, a cDNA was designed for the intracellular expression of the yeast tRNA Phe . Increasing amounts of the plasmid encoding tRNA Phe resulted in a corresponding increase in levels of yeast tRNA Phe in the cell. The yeast tRNA Phe isolated from cells transfected with the cDNA for yeast tRNA Phe , or in the cell lines expressing yeast tRNA Phe , were aminoacylated, indicating that the expressed yeast tRNA Phe was incorporated into tRNA biogenesis pathways and translation. Increasing the cytoplasmic levels of tRNA Phe resulted in increased encapsidation of tRNA Phe in viruses with a PBS complementary to tRNA Phe (psHIV-Phe) or tRNA Lys,3 (wild-type HIV-1). Production of infectious psHIV-Phe was dependent on the amount of cotransfected tRNA Phe cDNA. Increasing amounts of plasmids encoding yeast tRNA Phe produced an increase of infectious psHIV-Phe that plateaued at a level lower than that from the transfection of the wild-type genome, which uses tRNA Lys,3 as the primer for reverse transcription. Cell lines were generated that expressed yeast tRNA Phe at levels approximately 0.1% of that for tRNA Lys,3 . Even with this reduced level of yeast tRNA Phe , the cell lines complemented psHIV-Phe over background levels. The results of these studies demonstrate that intracellular levels of primer tRNA can have a direct effect on HIV-1 infectivity and further support the role for PBS-tRNA complementarity in the primer selection process

10 CFR 1304.114 - Responsibility for maintaining adequate safeguards.

Science.gov (United States)

2010-01-01

... the security and privacy of personal data. (4) The disposal and disposition of identifiable personal... contained in a system of records are adequately trained to protect the security and privacy of such records....114 Section 1304.114 Energy NUCLEAR WASTE TECHNICAL REVIEW BOARD PRIVACY ACT OF 1974 § 1304.114...

Small finger protein of avian and murine retroviruses has nucleic acid annealing activity and positions the replication primer tRNA onto genomic RNA.

Science.gov (United States)

Prats, A C; Sarih, L; Gabus, C; Litvak, S; Keith, G; Darlix, J L

1988-06-01

Retrovirus virions carry a diploid genome associated with a large number of small viral finger protein molecules which are required for encapsidation. Our present results show that finger protein p12 of Rous sarcoma virus (RSV) and p10 of murine leukaemia virus (MuLV) positions replication primer tRNA on the replication initiation site (PBS) at the 5' end of the RNA genome. An RSV mutant with a Val-Pro insertion in the finger motif of p12 is able to partially encapsidate genomic RNA but is not infectious because mutated p12 is incapable of positioning the replication primer, tRNATrp. Since all known replication competent retroviruses, and the plant virus CaMV, code for finger proteins analogous to RSV p12 or MuLV p10, the initial stage of reverse transcription in avian, mammalian and human retroviruses and in CaMV is probably controlled in an analogous way.

Need for Adequate Funding in the Administration of Secondary ...

African Journals Online (AJOL)

Funding is considered all over the world as the life wire that propels the educational sector towards achieving her objectives. The paper focuses on the need for adequate funding of secondary education in Nigeria. Emphases were laid on the alternative sources of funding for secondary schools as well as the consequences ...

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

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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.

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.

Near-UV stress in salmonella typhimurium: 4-thiouridine in tRNA, ppGpp, and ApppGpp as components of an adaptive response

International Nuclear Information System (INIS)

Kramer, G.F.; Baker, J.C.; Ames, B.N.

1988-01-01

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

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)

Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photoreactive uridine analogues

International Nuclear Information System (INIS)

Tanner, N.K.; Hanna, M.M.; Abelson, J.

1988-01-01

Yeast tRNA ligase, from Saccharomyces cerevisiae, is one of the protein components that is involved in the splicing reaction of intron-containing yeast precursor tRNAs. It is an unusual protein because it has three distinct catalytic activities. It functions as a polynucleotide kinase, as a cyclic phosphodiesterase, and as an RNA ligase. We have studied the binding interactions between ligase and precursor tRNAs containing two photoreactive uridine analogues, 4-thiouridine and 5-bromouridine. When irradiated with long ultraviolet light, RNA containing these analogues can form specific covalent bonds with associated proteins. In this paper, we show that 4-thiouridine triphosphate and 5-bromouridine triphosphate were readily incorporated into a precursor tRNA(Phe) that was synthesized, in vitro, with bacteriophage T7 RNA polymerase. The analogue-containing precursor tRNAs were authentic substrates for the two splicing enzymes that were tested (endonuclease and ligase), and they formed specific covalent bonds with ligase when they were irradiated with long-wavelength ultraviolet light. We have determined the position of three major cross-links and one minor cross-link on precursor tRNA(Phe) that were located within the intron and near the 3' splice site. On the basis of these data, we present a model for the in vivo splicing reaction of yeast precursor tRNAs

Do Online Bicycle Routing Portals Adequately Address Prevalent Safety Concerns?

Directory of Open Access Journals (Sweden)

Martin Loidl

2018-03-01

Full Text Available Safety concerns are among the most prevalent deterrents for bicycling. The provision of adequate bicycling infrastructure is considered as one of the most efficient means to increase cycling safety. However, limited public funding does not always allow agencies to implement cycling infrastructure improvements at the desirable level. Thus, bicycle trip planners can at least partly alleviate the lack of adequate infrastructure by recommending optimal routes in terms of safety. The presented study provides a systematic review of 35 bicycle routing applications and analyses to which degree they promote safe bicycling. The results show that most trip planners lack corresponding routing options and therefore do not sufficiently address safety concerns of bicyclists. Based on these findings, we developed recommendations on how to better address bicycling safety in routing portals. We suggest employing current communication technology and analysis to consider safety concerns more explicitly.

Developing a model for the adequate description of electronic communication in hospitals.

Science.gov (United States)

Saboor, Samrend; Ammenwerth, Elske

2011-01-01

Adequate information and communication systems (ICT) can help to improve the communication in hospitals. Changes to the ICT-infrastructure of hospitals must be planed carefully. In order to support a comprehensive planning, we presented a classification of 81 common errors of the electronic communication on the MIE 2008 congress. Our objective now was to develop a data model that defines specific requirements for an adequate description of electronic communication processes We first applied the method of explicating qualitative content analysis on the error categorization in order to determine the essential process details. After this, we applied the method of subsuming qualitative content analysis on the results of the first step. A data model for the adequate description of electronic communication. This model comprises 61 entities and 91 relationships. The data model comprises and organizes all details that are necessary for the detection of the respective errors. It can be for either used to extend the capabilities of existing modeling methods or as a basis for the development of a new approach.

Cognitive Attributes of Adequate and Inadequate Responders to Reading Intervention in Middle School

OpenAIRE

Miciak, Jeremy; Stuebing, Karla K.; Vaughn, Sharon; Roberts, Greg; Barth, Amy Elizabeth; Fletcher, Jack M.

2014-01-01

No studies have investigated the cognitive attributes of middle school students who are adequate and inadequate responders to Tier 2 reading intervention. We compared students in Grades 6 and 7 representing groups of adequate responders (n = 77) and inadequate responders who fell below criteria in (a) comprehension (n = 54); (b) fluency (n = 45); and (c) decoding, fluency, and comprehension (DFC; n = 45). These students received measures of phonological awareness, listening comprehension, rap...

12 CFR 1229.5 - Capital distributions for adequately capitalized Banks.

Science.gov (United States)

2010-01-01

... capitalized Banks. 1229.5 Section 1229.5 Banks and Banking FEDERAL HOUSING FINANCE AGENCY ENTITY REGULATIONS CAPITAL CLASSIFICATIONS AND PROMPT CORRECTIVE ACTION Federal Home Loan Banks § 1229.5 Capital... classification of adequately capitalized. A Bank may not make a capital distribution if such distribution would...

Region 10: Idaho Northern Ada County Adequate Letter (6/21/2013)

Science.gov (United States)

EPA approves motor vehicle emissions budget in the Northern Ada County PM10 State Implementation Plan, Maintenance Plan: Ten-Year Update for PM10 national ambient air quality standard, adequate for transportation conformity purposes.

48 CFR 52.216-29 - Time-and-Materials/Labor-Hour Proposal Requirements-Non-Commercial Item Acquisition With Adequate...

Science.gov (United States)

2010-10-01

...-Hour Proposal Requirements-Non-Commercial Item Acquisition With Adequate Price Competition. 52.216-29... Proposal Requirements—Non-Commercial Item Acquisition With Adequate Price Competition (FEB 2007) (a) The... Time-and-Materials/Labor-Hour Proposal Requirements—Non-Commercial Item Acquisition With Adequate Price...

[The human right to adequate food: an urban vision].

Science.gov (United States)

Casemiro, Juliana Pereira; Valla, Victor Vincent; Guimarães, Maria Beatriz Lisboa

2010-07-01

The human right to adequate food is comprehended in two dimensions: being free of hunger and denutrition and having access to an adequate food. The urban context, in which the possession of food is done primarily through merchandising because of its strong consuming appealing, became a big challenge to debate this topic in poor districts today. Here we combine considerations of a qualitative study carried out in São João de Meriti, Rio de Janeiro State, joining leaders from Pastoral da Criança in focal group sessions. The unemployment, the sub-employment and the difficulty in reaching the public health system, the social assistance and basic sanitation were presented as the major obstacles to bring into effect the human right to food. It was possible to determine that, among the strategies to fight the poverty and hunger, a big highlight is the establishment of mutual help mechanisms. The social support, generosity and religiousness were presented as the most important categories among the thoughts of the leaders. Facing a reality in which poverty and hunger appear as something inherent or become a mechanism of change during elections, the issue of the clienteles appears as a huge concern and challenge for those leaders.

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.

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.

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

Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation.

Science.gov (United States)

Fabrizio, Paola; Hoon, Shawn; Shamalnasab, Mehrnaz; Galbani, Abdulaye; Wei, Min; Giaever, Guri; Nislow, Corey; Longo, Valter D

2010-07-15

The study of the chronological life span of Saccharomyces cerevisiae, which measures the survival of populations of non-dividing yeast, has resulted in the identification of homologous genes and pathways that promote aging in organisms ranging from yeast to mammals. Using a competitive genome-wide approach, we performed a screen of a complete set of approximately 4,800 viable deletion mutants to identify genes that either increase or decrease chronological life span. Half of the putative short-/long-lived mutants retested from the primary screen were confirmed, demonstrating the utility of our approach. Deletion of genes involved in vacuolar protein sorting, autophagy, and mitochondrial function shortened life span, confirming that respiration and degradation processes are essential for long-term survival. Among the genes whose deletion significantly extended life span are ACB1, CKA2, and TRM9, implicated in fatty acid transport and biosynthesis, cell signaling, and tRNA methylation, respectively. Deletion of these genes conferred heat-shock resistance, supporting the link between life span extension and cellular protection observed in several model organisms. The high degree of conservation of these novel yeast longevity determinants in other species raises the possibility that their role in senescence might be conserved.

Establishing adequate conditions for mercury determination in environmental samples by INAA

International Nuclear Information System (INIS)

Perez, Caroline; Santos, Eliane C.; Saiki, Mitiko

2017-01-01

Mercury (Hg) is a toxic element released into the environment mainly by anthropic activities. Consequently, the improvement for Hg determination in environmental samples is of great interest. Instrumental Neutron Activation Analysis (INAA) is considered an adequate method to determine several elements. However, Hg determination by INAA is often hampered by its volatility, which causes losses. The aim of this study was to establish adequate irradiation conditions for Hg determination in environmental samples by INAA. The following parameters were evaluated: irradiation time, container for irradiation and spectral gamma ray interferences. For the study, aliquots of certified reference materials (CRMs) and tree bark samples were irradiated together with Hg synthetic standard at the IEA-R1 nuclear research reactor. Gamma ray activities of 1 97 Hg and 203 Hg were measured in a spectrometer coupled to a HGe detector. Results obtained indicated that polyethylene capsules or envelopes can be used as container for sample irradiation and the Hg impurities in these containers were negligible. Irradiation time of one hour was adequate for Hg determination and in long irradiations of 8 h problems of spectral interference of 198 Au and 75 Se were observed. In addition, Hg loss during the irradiation of 1 h and after irradiation was not observed. Quality control of Hg results, obtained in the CRMs analyses using one hour of irradiation, indicated good precision and accuracy with |Z score| < 2. The experimental conditions established in this study were applied to tree bark samples. Detection limits for Hg of these analyses were between 0.14 and 1.9 μg g -1 . (author)

Association of Circulating Transfer RNA fragments with antibody response to Mycoplasma bovis in beef cattle.

Science.gov (United States)

Casas, Eduardo; Cai, Guohong; Kuehn, Larry A; Register, Karen B; McDaneld, Tara G; Neill, John D

2018-03-13

High throughput sequencing allows identification of small non-coding RNAs. Transfer RNA Fragments are a class of small non-coding RNAs, and have been identified as being involved in inhibition of gene expression. Given their role, it is possible they may be involved in mediating the infection-induced defense response in the host. Therefore, the objective of this study was to identify 5' transfer RNA fragments (tRF5s) associated with a serum antibody response to M. bovis in beef cattle. The tRF5s encoding alanine, glutamic acid, glycine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with antibody response against M. bovis. tRF5s encoding alanine, glutamine, glutamic acid, glycine, histidine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with season, which could be attributed to calf growth. There were interactions (P < 0.05) between antibody response to M. bovis and season for tRF5 encoding selenocysteine (anticodon UGA), proline (anticodon CGG), and glutamine (anticodon TTG). Selenocysteine is a rarely used amino acid that is incorporated into proteins by the opal stop codon (UGA), and its function is not well understood. Differential expression of tRF5s was identified between ELISA-positive and negative animals. Production of tRF5s may be associated with a host defense mechanism triggered by bacterial infection, or it may provide some advantage to a pathogen during infection of a host. Further studies are needed to establish if tRF5s could be used as a diagnostic marker of chronic exposure.

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.

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

Enhanced antioxidant activity of gold nanoparticle embedded 3,6-dihydroxyflavone: a combinational study

Science.gov (United States)

Medhe, Sharad; Bansal, Prachi; Srivastava, Man Mohan

2014-02-01

The antioxidative effect of selected dietary compounds (3,6-dihydroxyflavone, lutein and selenium methyl selenocysteine) was determined in single and combination using DPPH (2,2-diphenyl-l-picrylhydrazyl), OH (hydroxyl), H2O2 (hydrogen peroxide) and NO (nitric oxide) radical scavenging assays. Radical scavenging effect of the dietary phytochemicals individually are found to be in the order: ascorbic acid (standard) > lutein > 3,6-dihydroxyflavone > selenium methyl selenocysteine, at concentration 100 μg/ml, confirmed by all the four bioassays (p nanotech enforcement of dietary phytochemicals shows the utility in the architecture of nanoparticle embedded phytoproducts having a wide range of applications in medical science.

Radiographic appearances following adequate transfusion in. beta. -thalassaemia

Energy Technology Data Exchange (ETDEWEB)

Scutellari, P.N.; Orzincolo, C.; Bagni, B.; Franceschini, F.

1989-01-01

The main lesions of the skull and hand, observed in a group of hypertransfused ..beta..-thalassaemic patients, are compared with a control group of low-transfused patients. Bony abnormalities reflect the relationship between proliferating bone marrow and bone cortex, and hypertransfusion therapy will prevent development of lesions only if established early in life. If this is done, the diploe in the skull may become normal, overgrowth of facial bones is moderate, pneumatisation of the paranasal sinuses is not completely prevented, and the 'hair-brush' pattern may disappear completely. A normal appearance of the hand in adequately treated patients differentiates between prepubertal patients and adults.

Importance of adequate exercise in the detection of coronary heart disease by radionuclide ventriculography

International Nuclear Information System (INIS)

Brady, T.J.; Thrall, J.H.; Lo, K.; Pitt, B.

1980-01-01

Rest and exercise radionuclide ventriculograms were obtained on 77 symptomatic patients without prior documented coronary artery disease (CAD). Coronary artery disease was present by angiograms in 48. Radionuclide ventriculography (RNV) was abnormal in 41 patients (overall sensitivity 85%). In 29 patients with normal coronary arteries, RNV was normal in 24 (specificity 83%). To determine if the exercise level affects sensitivity, the studies were graded for adequacy of exercise. It was considered adequate if patients developed (a) chest pain, or (b) ST segment depression of at least 1 mm, or (c) if they achieved a pressure rate product greater than 250. Among the 48 patients with coronary artery disease, 35 achieved adequate exercise. Thirty-three had an abnormal RNV (sensitivity 94%). In 13 patients who failed to achieve adequate exercise, RNV was abnormal in eight (sensitivity of only 62%). Some patients with coronary artery disease may have a normal ventricular response at inadequate levels of stress

Establishing adequate conditions for mercury determination in environmental samples by INAA

Energy Technology Data Exchange (ETDEWEB)

Perez, Caroline; Santos, Eliane C.; Saiki, Mitiko, E-mail: caroline.perez@usp.br [Instituto de Pesquisas Energéticas e Nucleares (IPEN/CNEN-SP), São Paulo, SP (Brazil)

2017-07-01

Mercury (Hg) is a toxic element released into the environment mainly by anthropic activities. Consequently, the improvement for Hg determination in environmental samples is of great interest. Instrumental Neutron Activation Analysis (INAA) is considered an adequate method to determine several elements. However, Hg determination by INAA is often hampered by its volatility, which causes losses. The aim of this study was to establish adequate irradiation conditions for Hg determination in environmental samples by INAA. The following parameters were evaluated: irradiation time, container for irradiation and spectral gamma ray interferences. For the study, aliquots of certified reference materials (CRMs) and tree bark samples were irradiated together with Hg synthetic standard at the IEA-R1 nuclear research reactor. Gamma ray activities of 1{sup 97}Hg and {sup 203}Hg were measured in a spectrometer coupled to a HGe detector. Results obtained indicated that polyethylene capsules or envelopes can be used as container for sample irradiation and the Hg impurities in these containers were negligible. Irradiation time of one hour was adequate for Hg determination and in long irradiations of 8 h problems of spectral interference of {sup 198}Au and {sup 75}Se were observed. In addition, Hg loss during the irradiation of 1 h and after irradiation was not observed. Quality control of Hg results, obtained in the CRMs analyses using one hour of irradiation, indicated good precision and accuracy with |Z score| < 2. The experimental conditions established in this study were applied to tree bark samples. Detection limits for Hg of these analyses were between 0.14 and 1.9 μg g{sup -1}. (author)

Anti-tumor effects of an engineered “killer” transfer RNA

International Nuclear Information System (INIS)

Zhou, Dong-hui; Lee, Jiyoung; Frankenberger, Casey; Geslain, Renaud; Rosner, Marsha; Pan, Tao

2012-01-01

Highlights: ► tRNA with anti-cancer effects. ► tRNA induced protein misfolding. ► tRNA as anti-tumor agent. -- Abstract: A hallmark of cancer cells is their ability to continuously divide; and rapid proliferation requires increased protein translation. Elevating levels of misfolded proteins can elicit growth arrest due to ER stress and decreased global translation. Failure to correct prolonged ER stress eventually results in cell death via apoptosis. tRNA Ser (AAU) is an engineered human tRNA Ser with an anticodon coding for isoleucine. Here we test the possibility that tRNA Ser (AAU) can be an effective killing agent of breast cancer cells and can effectively inhibit tumor-formation in mice. We found that tRNA Ser (AAU) exert strong effects on breast cancer translation activity, cell viability, and tumor formation. Translation is strongly inhibited by tRNA Ser (AAU) in both tumorigenic and non-tumorigenic cells. tRNA Ser (AAU) significantly decreased the number of viable cells over time. A short time treatment with tRNA Ser (AAU) was sufficient to eliminate breast tumor formation in a xenograft mouse model. Our results indicate that tRNA Ser (AAU) can inhibit breast cancer metabolism, growth and tumor formation. This RNA has strong anti-cancer effects and presents an opportunity for its development into an anti-tumor agent. Because tRNA Ser (AAU) corrupts the protein synthesis mechanism that is an integral component of the cell, it would be extremely difficult for tumor cells to evolve and develop resistance against this anti-tumor agent.

Predictors of Timely Prenatal Care Initiation and Adequate Utilization in a Sample of Late Adolescent Texas Latinas.

Science.gov (United States)

Torres, Rosamar; Kehoe, Priscilla; Heilemann, MarySue V

2018-03-01

Little is known of late adolescent Texas Latinas' prenatal care perceptions or how these perceptions predict timely prenatal care initiation or adequate utilization. Hence, the purpose of this study is to describe and compare these perceptions between participants with timely versus late prenatal care initiation and adequate, intermediate, and inadequate prenatal care utilization; and to determine predictors of timely prenatal care initiation and adequate utilization. Fifty-four postpartum Latinas were recruited through social media. Eligibility criteria were 18 to 21 years old, Texas-born, primiparous, uncomplicated pregnancy/delivery, and English literate. Prenatal care perceptions were measured with the Revised Better Babies Survey and Access Barriers to Care Index. Participants had favorable views of prenatal care benefits; however, not living with the baby's father predicted inadequate prenatal care, Wald χ 2 (1) = 4.93, p = .026. Perceived benefits of timely and adequate prenatal care predicted timely prenatal care initiation, χ 2 (1) = 7.47, p = .006. Self-reported depression during pregnancy predicted timely entry into prenatal care, χ 2 (1) = 4.73, p = .03. Participants' positive prenatal care perceptions did not predict adequate prenatal care utilization, indicating that barriers serve as powerful obstacles in late adolescent Texas Latinas.

Selenium. Role of the Essential Metalloid in Health

Science.gov (United States)

Kurokawa, Suguru; Berry, Marla J.

2015-01-01

Selenium is an essential micronutrient in mammals, but is also recognized as toxic in excess. It is a non-metal with properties that are intermediate between the chalcogen elements sulfur and tellurium. Selenium exerts its biological functions through selenoproteins. Selenoproteins contain selenium in the form of the 21st amino acid, selenocysteine (Sec), which is an analog of cysteine with the sulfur-containing side chain replaced by a Se-containing side chain. Sec is encoded by the codon UGA, which is one of three termination codons for mRNA translation in non-selenoprotein genes. Recognition of the UGA codon as a Sec insertion site instead of stop requires a Sec insertion sequence (SECIS) element in selenoprotein mRNAs and a unique selenocysteyl-tRNA, both of which are recognized by specialized protein factors. Unlike the 20 standard amino acids, Sec is biosynthesized from serine on its tRNA. Twenty-five selenoproteins are encoded in the human genome. Most of the selenoprotein genes were discovered by bioinformatics approaches, searching for SECIS elements downstream of in-frame UGA codons. Sec has been described as having stronger nucleophilic and electrophilic properties than cysteine, and Sec is present in the catalytic site of all selenoenzymes. Most selenoproteins, whose functions are known, are involved in redox systems and signaling pathways. However, several selenoproteins are not well characterized in terms of their function. The selenium field has grown dramatically in the last few decades, and research on selenium biology is providing extensive new information regarding its importance for human health. PMID:24470102

Implementation of selective prevention for cardiometabolic diseases; are Dutch general practices adequately prepared?

Science.gov (United States)

Stol, Daphne M; Hollander, Monika; Nielen, Markus M J; Badenbroek, Ilse F; Schellevis, François G; de Wit, Niek J

2018-03-01

Current guidelines acknowledge the need for cardiometabolic disease (CMD) prevention and recommend five-yearly screening of a targeted population. In recent years programs for selective CMD-prevention have been developed, but implementation is challenging. The question arises if general practices are adequately prepared. Therefore, the aim of this study is to assess the organizational preparedness of Dutch general practices and the facilitators and barriers for performing CMD-prevention in practices currently implementing selective CMD-prevention. Observational study. Dutch primary care. General practices. Organizational characteristics. General practices implementing selective CMD-prevention are more often organized as a group practice (49% vs. 19%, p = .000) and are better organized regarding chronic disease management compared to reference practices. They are motivated for performing CMD-prevention and can be considered as 'frontrunners' of Dutch general practices with respect to their practice organization. The most important reported barriers are a limited availability of staff (59%) and inadequate funding (41%). The organizational infrastructure of Dutch general practices is considered adequate for performing most steps of selective CMD-prevention. Implementation of prevention programs including easily accessible lifestyle interventions needs attention. All stakeholders involved share the responsibility to realize structural funding for programmed CMD-prevention. Aforementioned conditions should be taken into account with respect to future implementation of selective CMD-prevention. Key Points   There is need for adequate CMD prevention. Little is known about the organization of selective CMD prevention in general practices.   • The organizational infrastructure of Dutch general practices is adequate for performing most steps of selective CMD prevention.   • Implementation of selective CMD prevention programs including easily accessible

Response of cotton genotypes to boron under-b-adequate conditions

International Nuclear Information System (INIS)

Shah, J. A.; Sial, M. A.; Hassan, Z. U.; Rajpar, I.

2015-01-01

Balanced boron (B) application is well-known to enhance the cotton production; however, the narrow range between B-deficiency and toxicity levels makes it difficult to manage. Cotton genotypes extensively differ in their response to B requirements. The adequate dose of B for one genotype may be insufficient or even toxic to other genotype. The effects of boron (B) on seed cotton yield and its various yield associated traits were studied on 10 cotton genotypes of Pakistan. The pot studies were undertaken to categorize cotton genotypes using B-deficient (control) and B-adequate (2.0 kg B ha-1) levels arranged in CRD with four repeats. The results indicated that the seed cotton yield, yield attributes and B-uptake of genotypes were comparatively decreased in B-deficient stressed treatment. Genotype NIA-Ufaq exhibited wide range of adaptation and ranked as efficient-responsive, as it produced higher seed cotton yield under both B-regimes. SAU-2 and CIM-506 were highly-efficient and remaining all genotypes were medium-efficient. Genotype Sindh-1 produced low seed cotton yield under B deficient condition and ranked as low-efficient. B-efficient cotton genotypes can be grown in B deficient soils without B application. (author)

Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation.

Directory of Open Access Journals (Sweden)

Paola Fabrizio

2010-07-01

Full Text Available The study of the chronological life span of Saccharomyces cerevisiae, which measures the survival of populations of non-dividing yeast, has resulted in the identification of homologous genes and pathways that promote aging in organisms ranging from yeast to mammals. Using a competitive genome-wide approach, we performed a screen of a complete set of approximately 4,800 viable deletion mutants to identify genes that either increase or decrease chronological life span. Half of the putative short-/long-lived mutants retested from the primary screen were confirmed, demonstrating the utility of our approach. Deletion of genes involved in vacuolar protein sorting, autophagy, and mitochondrial function shortened life span, confirming that respiration and degradation processes are essential for long-term survival. Among the genes whose deletion significantly extended life span are ACB1, CKA2, and TRM9, implicated in fatty acid transport and biosynthesis, cell signaling, and tRNA methylation, respectively. Deletion of these genes conferred heat-shock resistance, supporting the link between life span extension and cellular protection observed in several model organisms. The high degree of conservation of these novel yeast longevity determinants in other species raises the possibility that their role in senescence might be conserved.

Uptake and speciation of selenium in garlic cultivated in soil amended with symbiotic fungi (mycorrhiza) and selenate

Energy Technology Data Exchange (ETDEWEB)

Larsen, Erik H.; Hansen, Marianne; Rasmussen, Peter Have; Sloth, Jens J. [Danish Institute for Food and Veterinary Research, Department of Food Chemistry, Soeborg (Denmark); Lobinski, Ryszard; Ruzik, Rafal; Mazurowska, Lena [CNRS UMR 5034, Pau (France); Warsaw University of Technology, Department of Analytical Chemistry, Warsaw (Poland); Burger-Meyer, Karin; Scholten, Olga [Wageningen University and Research Centre, Plant Research International (PRI), P.O. Box 16, Wageningen (Netherlands); Kik, Chris [Wageningen University and Research Centre, Plant Research International (PRI), P.O. Box 16, Wageningen (Netherlands); Wageningen University and Research Centre, Centre for Genetic Resources, The Netherlands (CGN), P.O. Box 16, Wageningen (Netherlands)

2006-07-15

The scope of the work was to investigate the influence of selenate fertilisation and the addition of symbiotic fungi (mycorrhiza) to soil on selenium and selenium species concentrations in garlic. The selenium species were extracted from garlic cultivated in experimental plots by proteolytic enzymes, which ensured liberation of selenium species contained in peptides or proteins. Separate extractions using an aqueous solution of enzyme-deactivating hydroxylamine hydrochloride counteracted the possible degradation of labile selenium species by enzymes (such as alliinase) that occur naturally in garlic. The selenium content in garlic, which was analysed by ICP-MS, showed that addition of mycorrhiza to the natural soil increased the selenium uptake by garlic tenfold to 15 {mu}g g{sup -1} (dry mass). Fertilisation with selenate and addition of mycorrhiza strongly increased the selenium content in garlic to around one part per thousand. The parallel analysis of the sample extracts by cation exchange and reversed-phase HPLC with ICP-MS detection showed that {gamma}-glutamyl-Se-methyl-selenocysteine amounted to 2/3, whereas methylselenocysteine, selenomethionine and selenate each amounted to a few percent of the total chromatographed selenium in all garlic samples. Se-allyl-selenocysteine and Se-propyl-selenocysteine, which are selenium analogues of biologically active sulfur-containing amino acids known to occur in garlic, were searched for but not detected in any of the extracts. The amendment of soil by mycorrhiza and/or by selenate increased the content of selenium but not the distribution of detected selenium species in garlic. Finally, the use of two-dimensional HPLC (size exclusion followed by reversed-phase) allowed the structural characterisation of {gamma}-glutamyl-Se-methyl-selenocysteine and {gamma}-glutamyl-Se-methyl-selenomethionine in isolated chromatographic fractions by quadrupole time-of-flight mass spectrometry. (orig.)

Selenoprotein P: an extracellular protein with unique physical characteristics and a role in selenium homeostasis.

Science.gov (United States)

Burk, Raymond F; Hill, Kristina E

2005-01-01

Selenoprotein P is an abundant extracellular glycoprotein that is rich in selenocysteine. It has two domains with respect to selenium content. The N-terminal domain of the rat protein contains one selenocysteine residue in a UxxC redox motif. This domain also has a pH-sensitive heparin-binding site and two histidine-rich amino acid stretches. The smaller C-terminal domain contains nine selenocysteine and ten cysteine residues. Four isoforms of selenoprotein P are present in rat plasma. They share the same N terminus and amino acid sequence. One isoform is full length and the three others terminate at the positions of the second, third, and seventh selenocysteine residues. Selenoprotein P turns over rapidly in rat plasma with the consequence that approximately 25% of the amount of whole-body selenium passes through it each day. Evidence supports functions of the protein in selenium homeostasis and oxidant defense. Selenoprotein P knockout mice have very low selenium concentrations in the brain, the testis, and the fetus, with severe pathophysiological consequences in each tissue. In addition, those mice waste moderate amounts of selenium in the urine. Selenoprotein P binds to endothelial cells in the rat, and plasma levels of the protein correlate with prevention of diquat-induced lipid peroxidation and hepatic endothelial cell injury. The mechanisms of these apparent functions remain speculative and much work on the mechanism of selenoprotein P function lies ahead. Measurement of selenoprotein P in human plasma has shown that it is depressed by selenium deficiency and by cirrhosis. Selenium supplementation of selenium-deficient human subjects showed that glutathione peroxidase activity was optimized before selenoprotein P concentration was optimized, indicating that plasma selenoprotein P is the better index of human selenium nutritional status.

Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis

International Nuclear Information System (INIS)

Eichert, André; Schreiber, Angela; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2009-01-01

Various E. coli tRNA Arg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis. The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA Arg , the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA Arg isoacceptors exist. In the present work, three different Escherichia coli tRNA Arg acceptor-stem helices were crystallized. Two of them, the tRNA Arg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNA Arg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNA Arg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°

Nuclear waste disposal: achieving adequate financing - special study

International Nuclear Information System (INIS)

Quasebarth, M.V.

1984-01-01

An analysis by the Congressional Budget Office (CBO) evaluates whether the current one mill fee now charged to nuclear-electricity consumers will adequately finance the waste disposal program. The CBO found that, if the fee is adjusted annually for inflation, it should provide enough revenues to cover all program costs under all nuclear growth forecasts. If the fee is unchanged, however, the fees will be inadequate if inflation exceeds 3% annually. The report suggests two alternatives for fee revision, but makes no recommendations. The alternatives are to increase the fee only at specific intervals or to automatically adjust the fee through indexation. The report examines the effect of delaying the program, cost overruns, and alternative inflation rate and interest rate assumptions. 3 figures, 12 tables

Rectal cancer delivery of radiotherapy in adequate time and with adequate dose is influenced by treatment center, treatment schedule, and gender and is prognostic parameter for local control: Results of study CAO/ARO/AIO-94

International Nuclear Information System (INIS)

Fietkau, Rainer; Roedel, Claus; Hohenberger, Werner; Raab, Rudolf; Hess, Clemens; Liersch, Torsten; Becker, Heinz; Wittekind, Christian; Hutter, Matthias; Hager, Eva; Karstens, Johann; Ewald, Hermann; Christen, Norbert; Jagoditsch, Michael; Martus, Peter; Sauer, Rolf

2007-01-01

Purpose: The impact of the delivery of radiotherapy (RT) on treatment results in rectal cancer patients is unknown. Methods and Materials: The data from 788 patients with rectal cancer treated within the German CAO/AIO/ARO-94 phase III trial were analyzed concerning the impact of the delivery of RT (adequate RT: minimal radiation RT dose delivered, 4300 cGy for neoadjuvant RT or 4700 cGy for adjuvant RT; completion of RT in <44 days for neoadjuvant RT or <49 days for adjuvant RT) in different centers on the locoregional recurrence rate (LRR) and disease-free survival (DFS) at 5 years. The LRR, DFS, and delivery of RT were analyzed as endpoints in multivariate analysis. Results: A significant difference was found between the centers and the delivery of RT. The overall delivery of RT was a prognostic factor for the LRR (no RT, 29.6% ± 7.8%; inadequate RT, 21.2% ± 5.6%; adequate RT, 6.8% ± 1.4%; p = 0.0001) and DFS (no RT, 55.1% ± 9.1%; inadequate RT, 57.4% ± 6.3%; adequate RT, 69.1% ± 2.3%; p = 0.02). Postoperatively, delivery of RT was a prognostic factor for LRR on multivariate analysis (together with pathologic stage) but not for DFS (independent parameters, pathologic stage and age). Preoperatively, on multivariate analysis, pathologic stage, but not delivery of RT, was an independent prognostic parameter for LRR and DFS (together with adequate chemotherapy). On multivariate analysis, the treatment center, treatment schedule (neoadjuvant vs. adjuvant RT), and gender were prognostic parameters for adequate RT. Conclusion: Delivery of RT should be regarded as a prognostic factor for LRR in rectal cancer and is influenced by the treatment center, treatment schedule, and patient gender

Factors Affecting the Presence of Adequately Iodized Salt at Home in Wolaita, Southern Ethiopia: Community Based Study.

Science.gov (United States)

Kumma, Wondimagegn Paulos; Haji, Yusuf; Abdurahmen, Junayde; Mehretie Adinew, Yohannes

2018-01-01

Universal use of iodized salt is a simple and inexpensive method to prevent and eliminate iodine deficiency disorders like mental retardation. However, little is known about the level of adequately iodized salt consumption in the study area. Therefore, the study was aimed at assessing the proportion of households having adequately iodized salt and associated factors in Wolaita Sodo town and its peripheries, Southern Ethiopia. A cross-sectional study was conducted from May 10 to 20, 2016, in 441 households in Sodo town and its peripheries. Samples were selected using the systematic sampling technique. An iodometric titration method (AOAC, 2000) was used to analyze the iodine content of the salt samples. Data entry and analysis were done using Epi Info version 3.5.1 and SPSS version 16, respectively. The female to male ratio of the respondents was 219. The mean age of the respondents was 30.2 (±7.3 SD). The proportion of households having adequately iodized salt was 37.7%, with 95% CI of 33.2% to 42.2%. Not exposing salt to sunlight with [OR: 3.75; 95% CI: 2.14, 6.57], higher monthly income [OR: 3.71; 95% CI: 1.97-7.01], and formal education of respondents with [OR: 1.75; 95% CI: 1.14, 2.70] were found associated with the presence of adequately iodized salt at home. This study revealed low levels of households having adequately iodized salt in Wolaita Sodo town and its peripheries. The evidence here shows that there is a need to increase the supply of adequately iodized salt to meet the goal for monitoring progress towards sustainable elimination of IDD.

Physiological aspect walking and Nordic walking as adequate kinetic activities.

OpenAIRE

BENEŠ, Václav

2010-01-01

This bachelor thesis on the topic of The Physiological Aspect of Walking and Nordic Walking as an adequate physical activity focuses on chosen physiological changes of an organism during a five-month training cycle. In the theoretical part I describe the physiological changes of organism during a regularly repeated strain, and also the technique of walking, Nordic walking and health benefits of these activities are defined here. The research part of the thesis describes the measurement method...

Self-esteem, social support, and satisfaction differences in women with adequate and inadequate prenatal care.

Science.gov (United States)

Higgins, P; Murray, M L; Williams, E M

1994-03-01

This descriptive, retrospective study examined levels of self-esteem, social support, and satisfaction with prenatal care in 193 low-risk postpartal women who obtained adequate and inadequate care. The participants were drawn from a regional medical center and university teaching hospital in New Mexico. A demographic questionnaire, the Coopersmith self-esteem inventory, the personal resource questionnaire part 2, and the prenatal care satisfaction inventory were used for data collection. Significant differences were found in the level of education, income, insurance, and ethnicity between women who received adequate prenatal care and those who received inadequate care. Women who were likely to seek either adequate or inadequate prenatal care were those whose total family income was $10,000 to $19,999 per year and high school graduates. Statistically significant differences were found in self-esteem, social support, and satisfaction between the two groups of women. Strategies to enhance self-esteem and social support have to be developed to reach women at risk for receiving inadequate prenatal care.

The impact of urban gardens on adequate and healthy food: a systematic review.

Science.gov (United States)

Garcia, Mariana T; Ribeiro, Silvana M; Germani, Ana Claudia Camargo Gonçalves; Bógus, Cláudia M

2018-02-01

To examine the impacts on food and nutrition-related outcomes resulting from participation in urban gardens, especially on healthy food practices, healthy food access, and healthy food beliefs, knowledge and attitudes. The systematic review identified studies by searching the PubMed, ERIC, LILACS, Web of Science and Embase databases. An assessment of quality and bias risk of the studies was carried out and a narrative summary was produced. Studies published as original articles in peer-reviewed scientific journals in English, Spanish or Portuguese between 2005 and 2015 were included. The studies included were based on data from adult participants in urban gardens. Twenty-four studies were initially selected based on the eligibility criteria, twelve of which were included. There was important heterogeneity of settings, population and assessment methods. Assessment of quality and bias risk of the studies revealed the need for greater methodological rigour. Most studies investigated community gardens and employed a qualitative approach. The following were reported: greater fruit and vegetable consumption, better access to healthy foods, greater valuing of cooking, harvest sharing with family and friends, enhanced importance of organic production, and valuing of adequate and healthy food. Thematic patterns related to adequate and healthy food associated with participation in urban gardens were identified, revealing a positive impact on practices of adequate and healthy food and mainly on food perceptions.

Structural organization of the transfer RNA operon I of Vibrio cholerae

Indian Academy of Sciences (India)

Nine major transfer RNA (tRNA) gene clusters were analysed in various Vibrio cholerae strains. Of these, only the tRNA operon I was found to differ significantly in V. cholerae classical (sixth pandemic) and El Tor (seventh pandemic) strains. Amongst the sixteen tRNA genes contained in this operon, genes for tRNA Gln3 ...

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.

Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.

Science.gov (United States)

Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Babu, I Ramesh; Chan, Clement T Y; Liu, Yuchen; Söll, Dieter; Blum, Paul; Kuwahara, Masayasu; Dedon, Peter C; Rajbhandary, Uttam L

2014-02-01

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.

Factors Affecting the Presence of Adequately Iodized Salt at Home in Wolaita, Southern Ethiopia: Community Based Study

Directory of Open Access Journals (Sweden)

Wondimagegn Paulos Kumma

2018-01-01

Full Text Available Background. Universal use of iodized salt is a simple and inexpensive method to prevent and eliminate iodine deficiency disorders like mental retardation. However, little is known about the level of adequately iodized salt consumption in the study area. Therefore, the study was aimed at assessing the proportion of households having adequately iodized salt and associated factors in Wolaita Sodo town and its peripheries, Southern Ethiopia. Methods. A cross-sectional study was conducted from May 10 to 20, 2016, in 441 households in Sodo town and its peripheries. Samples were selected using the systematic sampling technique. An iodometric titration method (AOAC, 2000 was used to analyze the iodine content of the salt samples. Data entry and analysis were done using Epi Info version 3.5.1 and SPSS version 16, respectively. Result. The female to male ratio of the respondents was 219. The mean age of the respondents was 30.2 (±7.3 SD. The proportion of households having adequately iodized salt was 37.7%, with 95% CI of 33.2% to 42.2%. Not exposing salt to sunlight with [OR: 3.75; 95% CI: 2.14, 6.57], higher monthly income [OR: 3.71; 95% CI: 1.97–7.01], and formal education of respondents with [OR: 1.75; 95% CI: 1.14, 2.70] were found associated with the presence of adequately iodized salt at home. Conclusion. This study revealed low levels of households having adequately iodized salt in Wolaita Sodo town and its peripheries. The evidence here shows that there is a need to increase the supply of adequately iodized salt to meet the goal for monitoring progress towards sustainable elimination of IDD.

Celebrating wobble decoding: Half a century and still much is new.

Science.gov (United States)

Agris, Paul F; Eruysal, Emily R; Narendran, Amithi; Väre, Ville Y P; Vangaveti, Sweta; Ranganathan, Srivathsan V

2017-08-16

A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.

Data Mining of Small RNA-Seq Suggests an Association Between Prostate Cancer and Altered Abundance of 5′ Transfer RNA Halves in Seminal Fluid and Prostatic Tissues

Directory of Open Access Journals (Sweden)

Joseph M Dhahbi

2018-02-01

Full Text Available Extracellular RNAs are gaining clinical interest as biofluid-based noninvasive markers for diseases, especially cancer. In particular, derivatives of transfer RNA (tRNA are emerging as a new class of small-noncoding RNAs with high biomarker potential. We and others previously reported alterations in serum levels of specific tRNA halves in disease states including cancer. Here, we explored seminal fluid for tRNA halves as potential markers of prostate cancer. We found that 5′ tRNA halves are abundant in seminal fluid and are elevated in prostate cancer relative to noncancer patients. Importantly, most of these tRNA halves are also detectable in prostatic tissues, and a subset were increased in malignant relative to adjacent normal tissue. These findings emphasize the potential of 5′ tRNA halves as noninvasive markers for prostate cancer screening and diagnosis and provide leads for future work to elucidate a putative role of the 5′ tRNA halves in carcinogenesis.

Transfer RNA and human disease

Directory of Open Access Journals (Sweden)

Jamie A Abbott

2014-06-01

Full Text Available Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA genes are hotspots for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase, mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers, and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing. Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

Transfer RNA and human disease.

Science.gov (United States)

Abbott, Jamie A; Francklyn, Christopher S; Robey-Bond, Susan M

2014-01-01

Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are "hotspots" for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

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.

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 been...

Follow-up of the ovarial carcinoma from the point of view of the gynecologist

International Nuclear Information System (INIS)

Vahrson, H.

1983-01-01

A co-operation between the different institutions and doctors and the tumor centre is indispensable for an adequate follow-up of the ovarial carcinoma. Besides diagnosis and therapy of side effects of the treatment as well as early diagnosis of recurrences, a psychical and social care is particularly necessary. The follow-up treatment aims at a full social rehabilitation of probably cured patients and, in case of incurable patients, at a relief of pain until death. The determination of t-RNA as a reliable tumor marker and the examinations necessary for routine controls (minimal and maximal programme) are indicated. (orig.) [de

HSQC-1,n-ADEQUATE: a new approach to long-range 13C-13C correlation by covariance processing.

Science.gov (United States)

Martin, Gary E; Hilton, Bruce D; Willcott, M Robert; Blinov, Kirill A

2011-10-01

Long-range, two-dimensional heteronuclear shift correlation NMR methods play a pivotal role in the assembly of novel molecular structures. The well-established GHMBC method is a high-sensitivity mainstay technique, affording connectivity information via (n)J(CH) coupling pathways. Unfortunately, there is no simple way of determining the value of n and hence no way of differentiating two-bond from three- and occasionally four-bond correlations. Three-bond correlations, however, generally predominate. Recent work has shown that the unsymmetrical indirect covariance or generalized indirect covariance processing of multiplicity edited GHSQC and 1,1-ADEQUATE spectra provides high-sensitivity access to a (13)C-(13) C connectivity map in the form of an HSQC-1,1-ADEQUATE spectrum. Covariance processing of these data allows the 1,1-ADEQUATE connectivity information to be exploited with the inherent sensitivity of the GHSQC spectrum rather than the intrinsically lower sensitivity of the 1,1-ADEQUATE spectrum itself. Data acquisition times and/or sample size can be substantially reduced when covariance processing is to be employed. In an extension of that work, 1,n-ADEQUATE spectra can likewise be subjected to covariance processing to afford high-sensitivity access to the equivalent of (4)J(CH) GHMBC connectivity information. The method is illustrated using strychnine as a model compound. Copyright © 2011 John Wiley & Sons, Ltd.

DoD Actions Were Not Adequate to Reduce Improper Travel Payments

Science.gov (United States)

2016-03-10

vouchers in near real time and identifies duplicate or incorrect payments. DoD Components developed corrective actions that did not include steps to...causes of improper payments. In addition, many of the payment errors were not preventable through real - time or post-payment automated validation checks...H 1 0 , 2 0 1 6 Report No. DODIG-2016-060 DoD Actions Were Not Adequate to Reduce Improper Travel Payments Mission Our mission is to provide

X-ray diffraction analysis of a human tRNAGly acceptor-stem microhelix isoacceptor at 1.18 Å resolution

International Nuclear Information System (INIS)

Eichert, André; Perbandt, Markus; Schreiber, Angela; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2008-01-01

The tRNA Gly acceptor-stem microhelix isoacceptor from human cytoplasm was crystallized and X-ray diffraction analysis revealed diffraction to 1.18 Å resolution. The sequence of the microhelix was derived from the gene sequence with tRNA Database ID DG9990. Interest has been focused on comparative X-ray structure analyses of different tRNA Gly acceptor-stem helices. tRNA Gly /glycyl-tRNA synthetase belongs to the so-called class II system, in which the tRNA identity elements consist of simple and unique determinants that are located in the tRNA acceptor stem and the discriminator base. Comparative structure investigations of tRNA Gly microhelices provide insight into the role of tRNA identity elements. Predominant differences in the structures of glycyl-tRNA synthetases and in the tRNA identity elements between prokaryotes and eukaryotes point to divergence during the evolutionary process. Here, the crystallization and high-resolution X-ray diffraction analysis of a human tRNA Gly acceptor-stem microhelix with sequence 5′-G 1 C 2 A 3 U 4 U 5 G 6 G 7 -3′, 5′-C 66 C 67 A 68 A 69 U 70 G 71 C 72 -3′ is reported. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 37.32, b = 37.61, c = 30.47 Å, β = 112.60° and one molecule per asymmetric unit. A data set was collected using synchrotron radiation and data were processed within the resolution range 50.0–1.18 Å. The structure was solved by molecular replacement

Gulf War Illnesses: DOD's Conclusions about U.S. Troops' Exposure Cannot Be Adequately Supported

National Research Council Canada - National Science Library

Rhodes, Keith

2004-01-01

... (MOD) conclusions about troops' exposure. The GAO found that DoD's and MOD's conclusions about troops' exposure to CW agents, based on DoD and CIA plume modeling, cannot be adequately supported...

The adequate rocuronium dose required for complete block of the adductor muscles of the thigh.

Science.gov (United States)

Fujimoto, M; Kawano, K; Yamamoto, T

2018-03-01

Rocuronium can prevent the obturator jerk during transurethral resection of bladder tumors. We investigated the adequate rocuronium dose required for complete block of the thigh adductor muscles, and its correlation with individual responses of the adductor pollicis muscle to rocuronium. Eleven patients scheduled for transurethral resection of bladder tumors under general anesthesia were investigated. After general anesthesia induction, neuromuscular monitoring of the adductor pollicis muscle and ultrasonography-guided stimulation of the obturator nerve was commenced. Rocuronium, 0.15 mg/kg, was repeatedly administered intravenously. The adequate rocuronium dose required for complete block of the thigh muscles, defined as the cumulative dose of rocuronium administered until that time, and its correlation with the first twitch response of the adductor pollicis muscle on train-of-four stimulation after initial rocuronium administration was analyzed. The rocuronium dose found adequate for complete block of the thigh muscles was 0.30 mg/kg in seven patients and 0.45 mg/kg in the remaining four patients, which did not correlate with the first twitch response. At the time of complete block of the thigh muscles, the neuromuscular blockade level of the adductor pollicis muscle varied greatly, although the level was never more profound than a post-tetanic count of 1. Although the response of the adductor pollicis muscle to rocuronium cannot be used to determine the adequate rocuronium dose required for complete block of the thigh muscles, intense blockade, with maintenance of post-tetanic count at ≤ 1 in the adductor pollicis muscle is essential to prevent the obturator jerk. © 2017 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

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.

33 CFR 155.4050 - Ensuring that the salvors and marine firefighters are adequate.

Science.gov (United States)

2010-07-01

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Ensuring that the salvors and marine firefighters are adequate. 155.4050 Section 155.4050 Navigation and Navigable Waters COAST GUARD..., water turbidity, water depth, sea state and temperature extremes). (13) Resource provider has the...

Does Current Army Physical Fitness Training Doctrine Adequately Prepare Soldiers for War?

Science.gov (United States)

2010-06-11

longer 7 adequate to sustain the activity. Anaerobic activities include sprinting, soccer , and basketball. Balance: The ability to maintain...deep muscles, and joint articulations. The common push-up requires the interaction of 21 different muscles to execute one repetition. The overhead press...aerobically break down glycogen, carbohydrates , and fats to produce energy. The more regularly the individual conducts cardio-respiratory training

A student's perspective: are medical students adequately trained in BLS?

Directory of Open Access Journals (Sweden)

Oyewole T

2016-11-01

Full Text Available Tobi Oyewole,1 Folashade Oyewole2 1University of Liverpool – The School of Medicine, Liverpool, 2Imperial College London, London, UK We read with great interest the article by Lami et al regarding improving basic life support (BLS training for medical students.1 We agree that BLS skills are vital for junior doctors. The days of trial by fire have long gone away, and junior doctors and medical students need to feel that they are adequately trained to handle emergency situations they may face in hospital.  Read the original article

[The pregnant employee in anaesthesia and intensive care - An evidence-based approach to designing adequate workplaces].

Science.gov (United States)

Röher, Katharina; Göpfert, Matthias S

2015-07-01

In the light of a rising percentage of women among employees in anaesthesia and intensive care designing adequate workplaces for pregnant employees plays an increasingly important role. Here it is necessary to align the varied interests of the pregnant employee, fellow employees and the employer, where the legal requirements of the Maternity Protection Act ("Mutterschutzgesetz") form the statutory framework. This review describes how adequate workplaces for pregnant employees in anaesthesia and intensive care can be established considering the scientific evidence on the subject. © Georg Thieme Verlag Stuttgart · New York.

Selenium and Selenoprotein Deficiencies Induce Widespread Pyogranuloma Formation in Mice, while High Levels of Dietary Selenium Decrease Liver Tumor Size Driven by TGFα

Science.gov (United States)

Zhong, Nianxin; Ward, Jerrold M.; Perella, Christine M.; Hoffmann, Victoria J.; Rogers, Keith; Combs, Gerald F.; Schweizer, Ulrich; Merlino, Glenn; Gladyshev, Vadim N.; Hatfield, Dolph L.

2013-01-01

Changes in dietary selenium and selenoprotein status may influence both anti- and pro-cancer pathways, making the outcome of interventions different from one study to another. To characterize such outcomes in a defined setting, we undertook a controlled hepatocarcinogenesis study involving varying levels of dietary selenium and altered selenoprotein status using mice carrying a mutant (A37G) selenocysteine tRNA transgene (TrsptG37) and/or a cancer driver TGFα transgene. The use of TrsptG37 altered selenoprotein expression in a selenoprotein and tissue specific manner and, at sufficient dietary selenium levels, separate the effect of diet and selenoprotein status. Mice were maintained on diets deficient in selenium (0.02 ppm selenium) or supplemented with 0.1, 0.4 or 2.25 ppm selenium or 30 ppm triphenylselenonium chloride (TPSC), a non-metabolized selenium compound. TrsptG37 transgenic and TGFα/TrsptG37 bi-transgenic mice subjected to selenium-deficient or TPSC diets developed a neurological phenotype associated with early morbidity and mortality prior to hepatocarcinoma development. Pathology analyses revealed widespread disseminated pyogranulomatous inflammation. Pyogranulomas occurred in liver, lungs, heart, spleen, small and large intestine, and mesenteric lymph nodes in these transgenic and bi-transgenic mice. The incidence of liver tumors was significantly increased in mice carrying the TGFα transgene, while dietary selenium and selenoprotein status did not affect tumor number and multiplicity. However, adenoma and carcinoma size and area were smaller in TGFα transgenic mice that were fed 0.4 and 2.25 versus 0.1 ppm of selenium. Thus, selenium and selenoprotein deficiencies led to widespread pyogranuloma formation, while high selenium levels inhibited the size of TGFα–induced liver tumors. PMID:23460847

Towards 31Mg-β-NMR resonance linewidths adequate for applications in magnesium chemistry

DEFF Research Database (Denmark)

Stachura, M.; McFadden, R. M. L.; Chatzichristos, A.

2017-01-01

The span of most chemical shifts recorded in conventional 25Mg-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 31Mg- β-NMR measurements of 31Mg+ ions implanted...

Incentives for an adequate, economic and reliable Swiss transmission grid. Final version

International Nuclear Information System (INIS)

Twomey, P.; Neuhoff, K.; Newbery, D.

2006-11-01

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

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

The role of Glu259 in Escherichia coli elongation factor Tu in ternary complex formation

DEFF Research Database (Denmark)

Nautrup Pedersen, Gitte; Rattenborg, Thomas; Knudsen, Charlotte Rohde

1998-01-01

Determination of the crystal structure of the ternary complex formed between elongation factor Tu:GTP and aminoacylated tRNA revealed three regions of interaction between elongation factor Tu and tRNA. The structure indicates that the conserved glutamic acid at position 271 in Thermus aquaticus EF-Tu...... could be involved in the binding of the 3' CCA-Phe end of the aminoacylated tRNA. Therefore, the corresponding residue, Glu259, of Escherichia coli EF-Tu was mutated into alanine, aspartic acid, glutamine and tyrosine, in order to substantiate the crystallographic structural evidence and to obtain...... of interaction with tRNA, while mutation to tyrosine abolished completely the interaction with tRNA. Finally, mutation to glutamine resulted in an elongation factor Tu variant behaving like the wild type. In conclusion, the environment around the site binding the CCA-Phe end of the tRNA is very restricted...

Crystallization and preliminary X-ray diffraction analysis of a tRNASer acceptor-stem microhelix

International Nuclear Information System (INIS)

Förster, Charlotte; Krauss, Norbert; Brauer, Arnd B. E.; Szkaradkiewicz, Karol; Brode, Svenja; Hennig, Klaus; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.

2006-01-01

In order to investigate tRNA identity elements, an elongator tRNA Ser acceptor-stem helix was crystallized and a data set was collected to 1.8 Å resolution aiming at a comparison with the corresponding region in suppressor tRNA Sec . In order to understand elongator tRNA Ser and suppressor tRNA Sec identity elements, the respective acceptor-stem helices have been synthesized and crystallized in order to analyse and compare their structures in detail at high resolution. The synthesis, crystallization and preliminary X-ray diffraction results for a seven-base-pair tRNA Ser acceptor-stem helix are presented here. Diffraction data were collected to 1.8 Å, applying synchrotron radiation and cryogenic cooling. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 36.14, b = 38.96, c = 30.81 Å, β = 110.69°

Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli.

Science.gov (United States)

Björk, G R; Neidhardt, F C

1975-10-01

Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli. Ordinary measurements of growth rate in different media revealed no effect of the loss of m5U in tRNA. A gene located close to trmA (the structural cistron for the methyltransferase that produces m5U in tRNA), however, was found to reduce the growth rates significantly, depending on the medium and the temperature of cultivation. Measurement of codon recognition, macromolecular composition, tRNA binding to the ribosome, and the rate of protein chain elongation in vivo indicated no disadvantage caused by the lack of m5U. The regulation of ilv and his operons seemed also to be unaffected by the absence of m5U in the tRNA. In a mixed population experiment, however, cells possessing m5U in their tRNA seemed to have a distinct advantage over cells lacking this modified nucleoside. This experiment provides the first indication of the overall value of m5U in tRNA.

Adequate Education: Issues in Its Definition and Implementation. School Finance Project, Working Papers.

Science.gov (United States)

Tron, Esther, Ed.

Section 1203 of the Education Amendments of 1978 mandated the undertaking of studies concerning the adequate financing of elementary and secondary education in the 1980s. Created to carry out this mandate, the School Finance Project established as one of its goals reporting to Congress on issues implicit in funding educational adequacy. Several…

Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9.

Science.gov (United States)

Jackman, Jane E; Montange, Rebecca K; Malik, Harmit S; Phizicky, Eric M

2003-05-01

Methylation of tRNA at the N-1 position of guanosine to form m(1)G occurs widely in nature. It occurs at position 37 in tRNAs from all three kingdoms, and the methyltransferase that catalyzes this reaction is known from previous work of others to be critically important for cell growth in Escherichia coli and the yeast Saccharomyces cerevisiae. m(1)G is also widely found at position 9 in eukaryotic tRNAs, but the corresponding methyltransferase was unknown. We have used a biochemical genomics approach with a collection of purified yeast GST-ORF fusion proteins to show that m(1)G(9) formation of yeast tRNA(Gly) is associated with ORF YOL093w, named TRM10. Extracts lacking Trm10p have undetectable levels of m(1)G(9) methyltransferase activity but retain normal m(1)G(37) methyltransferase activity. Yeast Trm10p purified from E. coli quantitatively modifies the G(9) position of tRNA(Gly) in an S-adenosylmethionine-dependent fashion. Trm10p is responsible in vivo for most if not all m(1)G(9) modification of tRNAs, based on two results: tRNA(Gly) purified from a trm10-Delta/trm10-Delta strain is lacking detectable m(1)G; and a primer extension block occurring at m(1)G(9) is removed in trm10-Delta/trm10-Delta-derived tRNAs for all 9 m(1)G(9)-containing species that were testable by this method. There is no obvious growth defect of trm10-Delta/trm10-Delta strains. Trm10p bears no detectable resemblance to the yeast m(1)G(37) methyltransferase, Trm5p, or its orthologs. Trm10p homologs are found widely in eukaryotes and many archaea, with multiple homologs in several metazoans, including at least three in humans.

Long-Term Recurrent Subarachnoid Hemorrhage After Adequate Coiling Versus Clipping of Ruptured Intracranial Aneurysms

NARCIS (Netherlands)

Schaafsma, Joanna D.; Sprengers, Marieke E.; van Rooij, Willem Jan; Sluzewski, Menno; Majoie, Charles B. L. M.; Wermer, Marieke J. H.; Rinkel, Gabriel J. E.

Background and Purpose-Coiling is increasingly used as treatment for intracranial aneurysms. Despite its favorable short-term outcome, concerns exist about long-term reopening and inherent risk of recurrent subarachnoid hemorrhage (SAH). We hypothesized a higher risk for recurrent SAH after adequate

Transfer RNA methylases in rat placenta

International Nuclear Information System (INIS)

Jagtiani, S.K.; Narurkar, L.M.; Narurkar, M.V.

1977-01-01

Presence of tRNA methylases (5-adenosylmethionine : tRNA methyltransferases) was demonstrated at various stages of gestation in rat placenta, the enzyme being 50-100% higher than that of adult rat liver during early gestation. Placental tRNA methylases were shown to differ from those of liver in the extent of methylation. Glycine methyltransferase (S-adenosylmethionine : glycine methyltransferase), a regulatory enzyme in adult rat liver, was absent in placenta throughout gestation. The placental tRNA methylases could be inhibited in vitro by semipurified glycine methyltransferase from adult rat liver. The high placental tRNA methylase activity was comparable with the inhibitor-free enzyme activity of the adult rat liver. S-adenosyl-[Me- 14 C]-methionine was used in the investigation. (author)

Recognition of tRNAs with a long variable arm by aminoacyl-tRNA synthetases

Directory of Open Access Journals (Sweden)

Tukalo M. A.

2013-07-01

Full Text Available In prokaryotic cells three tRNA species, tRNASer, tRNALeu and tRNATyr, possess a long variable arm of 11–20 nucleotides (type 2 tRNA rather than usual 4 or 5 nucleotides (type 1 tRNA. In this review we have summarized the results of our research on the structural basis for recognition and discrimination of type 2 tRNAs by Thermus thermophilus seryl-, tyrosyl- and leucyl-tRNA synthetases (SerRS, TyrRS and LeuRS obtained by X-ray crystallography and chemical probing tRNA in solution. Crystal structures are now known of all three aminoacyl-tRNA synthetases complexed with type 2 tRNAs and the different modes of tRNA recognition represented by these structures will be discussed. In particular, emphasis will be given to the results on recognition of characteristic shape of type 2 tRNAs by cognate synthetases. In tRNASer, tRNATyr and tRNALeu the orientation of the long variable arm with respect to the body of the tRNA is different and is controlled by different packing of the core. In the case of SerRS the N-terminal domain and in the case of TyrRS, the C-terminal domain, bind to the characteristic long variable arm of the cognate RNA, thus recognizing the unique shape of the tRNA. The core of T. thermophilus tRNALeu has several layers of unusual base-pairs, which are revealed by the crystal structure of tRNALeu complexed with T. thermophilus LeuRS and by probing a ligand-free tRNA by specific chemical reagents in solution. In the crystal structure of the LeuRS-tRNALeu complex the unique D-stem structure is recognized by the C-terminal domain of LeuRS and these data are in good agreement with those obtained in solution. LeuRS has canonical class I mode of tRNA recognition, approaching the tRNA acceptor stem from the D-stem and minor groove of the acceptor stem side. SerRS also has canonical class II mode of tRNA recognition and approaches tRNASer from opposite, variable stem and major groove of acceptor stem site. And finally, TyrRS in strong

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

DEFF Research Database (Denmark)

Parlesak, A.; Tetens, Inge; Dejgård Jensen, Jørgen

2016-01-01

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 ...

SIMS of transfer ribonucleic acid molecules encapsulated between free-standing graphene sheets.

Science.gov (United States)

Verkhoturov, Dmitriy S; Geng, Sheng; Verkhoturov, Stanislav V; Kim, Hansoo; Schweikert, Emile A

2016-06-01

In this study, the authors used cluster-secondary ion mass spectrometry method to investigate the preserved transfer ribonucleic acid (tRNA) encapsulated between two free-standing graphene sheets. Single impacts of 50 keV C60 (2+) projectiles generated the emission of tRNA fragment ions in the transmission direction for mass selection and detection in a time-of-flight mass spectrometer. Ribonucleic acid (RNA) is extremely unstable and prone to rapid enzymatic degradation by ribonucleases. Employing graphene to isolate RNA from the environment, the authors prevent the aforementioned process. Encapsulation was achieved by drop casting a solution of tRNA, prepared using deuterated water, onto one graphene sheet and covering it with another. The event-by-event bombardment/detection mode allowed us to use colocalization analysis method to characterize the tRNA and its immediate environment. The authors found that upon drying, tRNA agglomerated into nanostructures ∼60 nm in diameter via formation and subsequent drying of aqua cells. The tRNA nanoagglomerates had a density of ∼42 structures per μm(2) with coverage of ∼12% of the surface area. In addition, trace amounts of water remained mostly around the tRNA nanoagglomerates, probably in the form of hydration.

Bacterial Growth Physiology

DEFF Research Database (Denmark)

Kongstad, Mette

level of tRNA that the tRNA level was seemingly reduced much faster than observed before, after the induction of amino acid starvation. Therefore, we developed a method for testing this observation. It turned out that tRNA degrades to ~75% of the initial level within 40 minutes after induction of amino...

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.

Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

Science.gov (United States)

Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En-Duo; Giegé, Richard; Lin, Sheng-Xiang

2018-05-25

Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNA Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNAGly acceptor-stem microhelix

International Nuclear Information System (INIS)

Förster, Charlotte; Perbandt, Markus; Brauer, Arnd B. E.; Brode, Svenja; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.

2006-01-01

In order to investigate the identity elements of the E. coli tRNA Gly /GlyRS class II system, a tRNA Gly acceptor-stem microhelix was crystallized and a data set was collected to 2.0 Å resolution using synchrotron radiation. The tRNA Gly and glycyl-tRNA synthetase (GlyRS) system is an evolutionary special case within the class II aminoacyl-tRNA synthetases because two divergent types of GlyRS exist: an archaebacterial/human type and an eubacterial type. The tRNA identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of tRNA Gly . To obtain further insight concerning structural investigation of the identity elements, the Escherichia coli seven-base-pair tRNA Gly acceptor-stem helix was crystallized. Data were collected to 2.0 Å resolution using synchrotron radiation. Crystals belong to space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 35.35, c = 130.82 Å, α = β = 90, γ = 120° and two molecules in the asymmetric unit

Search for adequate quality standards for neutron radiography of nuclear fuel

International Nuclear Information System (INIS)

Domanus, J.C.

1983-01-01

Unlike in other fields of industrial radiography, where standard methods and procedures are used to control the quality of the radiographic image, no such standard exists for neutron radiography of nuclear fuel. To fill that gap it was felt that standardization work ought to be started in that field, too. Accordingly in 1979 an Euratom Neutron Radiography Working Group was constituted, which initiated standardization work in the field of neutron radiography of nuclear fuel. Finding adequate standards for image quality of neutron radiographs and checking the accuracy of dimension measurements from them were given first priority. (Auth.)

Can Earth Materials BE Adequately Covered in a - or Two-Semester Course?

Science.gov (United States)

Hefferan, K. P.; O'Brien, J.

2007-12-01

Traditional geology programs offer courses in mineralogy, optical mineralogy, igneous petrology, metamorphic petrology, sedimentology and economic geology. At many universities this suite of mineralogy/petrology courses has been supplanted by a one-semester or two-semester Earth Materials course. This interactive poster poses five questions to faculty and students related to the means by which Earth Materials can be delivered: 1) Available online syllabi demonstrate a wide variation in the topics addressed in Earth Materials courses; is there a standard core of key topics that must be covered and in what level of detail? 2) Can a one-semester or two- semester Earth Materials course adequately cover these topics? 3) Excellent textbooks exist in both mineralogy and in petrology; what textbooks, if any, adequately encompass Earth Materials? 4) How has the online environment changed the way in which we use textbooks in the classroom? 5) Given the evolution of geology programs, higher education and the global economy in the past twenty years, what additional changes can be anticipated with respect to delivery and demand of Earth Materials topics? Answers-- or at least related discussions-- to these questions are encouraged via verbal dialogue among participants and/or by comments written on the poster. Our goal is to solicit faculty, student and industry feedback to create a textbook, curricula and online materials that support an Earth Materials course.

Enhancing entrepreneurship development in Bosnia and Herzegovina through adequate governmental financial support

Directory of Open Access Journals (Sweden)

Bahrija Umihanić

2016-06-01

Full Text Available Entrepreneurship and SME sector is extremely important for general economic development in Bosnia and Herzegovina. In order to enhance further development of the SME sector adequate sources of financing for businesses need to be available and accessible. Entrepreneurs and owners of small and medium businesses in Bosnia and Herzegovina are facing certain challenges in obtaining finances. The issue of accessing sources of finance for SMEs in this country has remained problematic for years. Many relevant studies worldwide emphasise the importance of adequate sources of financing entrepreneurship and SME development. However, a variety of factors influence financing of SMEs depending on the region, economic development, development of financial markets etc. In this paper the authors are addressing the problem of financing SMEs focusing on the governmental support, with emphasis on Bosnia and Herzegovina. The main aim of the paper is to provide an answer to the question whether the government support in Bosnia and Herzegovina enables SMEs to access initial financing, needed for their entrepreneurial activity. The paper presents results of an empirical research conducted among managers of SMEs in Bosnia and Herzegovina in regards to availability and adequacy of financial products for these businesses. The results indicate that entrepreneurs in B&H rarely use government funds as a source of financing business activities, which is mostly caused by insufficient funds and inefficient government procedures.

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.

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...

[Investigation into the relationship between mitochondrial 12 S rRNA gene, tRNA gene and cytochrome oxidase Ⅱ gene variations and the risk of noise-induced hearing loss].

Science.gov (United States)

Jiao, J; Gu, G Z; Chen, G S; Li, Y H; Zhang, H L; Yang, Q Y; Xu, X R; Zhou, W H; Wu, H; He, L H; Zheng, Y X; Yu, S F

2017-01-06

Objective: To explore the relationship between mitochondrial 12 S rRNA gene variation, tRNA gene variation and cytochrome oxidase Ⅱ gene point mutations and the risk of noise-induced hearing loss (NIHL). Methods: A nested case-control study was performed that followed a cohort of 7 445 noise-exposed workers in a steel factory in Henan province, China, from January 1, 2006 to December 31, 2015. Subjects whose average hearing threshold was more than 40 dB(A) in high frequency were defined as the case group, and subjects whose average hearing threshold was less than 35 dB(A) in high frequency and less than 25 dB (A) in speech frequency were defined as the control group. Subjects was recruited into the case group ( n =286) and the control group ( n= 286) according to gender, age, job category and time of exposure to noise, and a 1∶1 case-control study was carried out. We genotyped eight single nucleotide polymorphisms in the mitochondrial 12 S rRNA gene, the mitochondrial tRNA gene and the mitochondrial cytochrome oxidase Ⅱ gene using SNPscan high-throughput genotyping technology from the recruited subjects. The relationship between polymorphic sites and NIHL, adjusted for covariates, was analyzed using conditional logistic regression analysis, as were the subgroup data. Results: The average age of the recruited subjects was (40.3±8.1) years and the length of service exposure to noise was (18.6±8.9) years. The range of noise exposed levels and cumulative noise exposure (CNE) was 80.1- 93.4 dB (A) and 86.8- 107.9 dB (A) · year, respectively. For workers exposed to noise at a CNE level<98 dB (A) · year, smokers showed an increased risk of NIHL of 1.88 (1.16-3.05) compared with non-smokers; for workers exposed to noise at a CNE level ≥98 dB(A) · year, smokers showed an increased risk of NIHL of 2.53 (1.49- 4.30) compared with non-smokers. For workers exposed to noise at a CNE level<98 dB (A) · year, the results of univariate analysis and multifactor analysis

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

Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis.

Science.gov (United States)

Gan, Qinglei; Fan, Chenguang

2017-11-01

Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position. By removing three near cognate tRNA isoacceptors of the amber stop codon [tRNA Lys , tRNA Tyr , and tRNA Gln (CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved. Removal of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems. We provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. 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 © 2016 Elsevier B.V. All rights reserved.

3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNA^Lys(UUU) from Trypanosoma brucei

DEFF Research Database (Denmark)

Krog, Jesper Schak; Español, Yaiza; Giessing, Anders M B

2011-01-01

tRNA is the most heavily modified of all RNA types, with typically 10-20% of the residues being post-transcriptionally altered. Unravelling the modification pattern of a tRNA is a challenging task; there are 92 currently known tRNA modifications [1], many of which are chemically similar. Furtherm......tRNA is the most heavily modified of all RNA types, with typically 10-20% of the residues being post-transcriptionally altered. Unravelling the modification pattern of a tRNA is a challenging task; there are 92 currently known tRNA modifications [1], many of which are chemically similar...... of the unmodified tRNA revealed the modified residues. The modifications were further characterized at the nucleoside level by chromatographic retention time and fragmentation pattern upon higher-order tandem MS. Phylogenetic comparison with modifications in tRNA(Lys) from other organisms was used through......: a minor fraction with the previously described 2-methylthio-N(6) -threonylcarbamoyl-modification, and a major fraction with A37 being modified by a 294.0-Da moiety. The latter product is the largest adenosine modification reported so far, and we discuss its nature and origin....

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

Science.gov (United States)

2011-08-17

...] Hemoglobin Standards and Maintaining Adequate Iron Stores in Blood Donors; Public Workshop AGENCY: Food and... Donors.'' The purpose of this public workshop is to discuss blood donor hemoglobin and hematocrit qualification standards in the United States, its impact on donor safety and blood availability, and potential...

Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA

International Nuclear Information System (INIS)

Soler, Nicolas; Fourmy, Dominique; Yoshizawa, Satoko

2007-01-01

The mRNA-binding domain of E. coli selenocysteine-specific elongation factor SelB (residues 478–614; SelB-WH3/4) was overproduced in E. coli and its cognate mRNA ligand, 23 nucleotides of the SECIS RNA hairpin, was prepared by in vitro transcription. The purified SelB-WH3/4–SECIS RNA complex crystallized in space group C2 and diffracted to 2.3 Å. In bacteria, selenocysteine (the 21st amino acid) is incorporated into proteins via machinery that includes SelB, a specific translational elongation factor. SelB binds to an mRNA hairpin called the selenocysteine-insertion sequence (SECIS) and delivers selenocysteyl-tRNA Sec to the ribosomal A site. The minimum C-terminal fragment (residues 478–614) of Escherichia coli SelB (SelB-WH3/4) required for SECIS binding has been overexpressed and purified. This protein was crystallized in complex with 23 nucleotides of the SECIS hairpin at 294 K using the hanging-drop vapour-diffusion method. A data set was collected to 2.3 Å resolution from a single crystal at 100 K using ESRF beamline BM-30. The crystal belongs to space group C2, with unit-cell parameters a = 103.50, b = 56.51, c = 48.41 Å. The asymmetric unit contains one WH3/4-domain–RNA complex. The Matthews coefficient was calculated to be 3.37 Å 3 Da −1 and the solvent content was estimated to be 67.4%

The role of electrostatics in TrxR electron transfer mechanism: A computational approach.

Science.gov (United States)

Teixeira, Vitor H; Capacho, Ana Sofia C; Machuqueiro, Miguel

2016-12-01

Thioredoxin reductase (TrxR) is an important enzyme in the control of the intracellular reduced redox environment. It transfers electrons from NADPH to several molecules, including its natural partner, thioredoxin. Although there is a generally accepted model describing how the electrons are transferred along TrxR, which involves a flexible arm working as a "shuttle," the molecular details of such mechanism are not completely understood. In this work, we use molecular dynamics simulations with Poisson-Boltzmann/Monte Carlo pKa calculations to investigate the role of electrostatics in the electron transfer mechanism. We observed that the combination of redox/protonation states of the N-terminal (FAD and Cys59/64) and C-terminal (Cys497/Selenocysteine498) redox centers defines the preferred relative positions and allows for the flexible arm to work as the desired "shuttle." Changing the redox/ionization states of those key players, leads to electrostatic triggers pushing the arm into the pocket when oxidized, and pulling it out, once it has been reduced. The calculated pKa values for Cys497 and Selenocysteine498 are 9.7 and 5.8, respectively, confirming that the selenocysteine is indeed deprotonated at physiological pH. This can be an important advantage in terms of reactivity (thiolate/selenolate are more nucleophilic than thiol/selenol) and ability to work as an electrostatic trigger (the "shuttle" mechanism) and may be the reason why TrxR uses selenium instead of sulfur. Proteins 2016; 84:1836-1843. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Zinc content of selected tissues and taste perception in rats fed zinc deficient and zinc adequate rations

International Nuclear Information System (INIS)

Boeckner, L.S.; Kies, C.

1986-01-01

The objective of the study was to determine the effects of feeding zinc sufficient and zinc deficient rations on taste sensitivity and zinc contents of selected organs in rats. The 36 Sprague-Dawley male weanling rats were divided into 2 groups and fed zinc deficient or zinc adequate rations. The animals were subjected to 4 trial periods in which a choice of deionized distilled water or a solution of quinine sulfate at 1.28 x 10 -6 was given. A randomized schedule for rat sacrifice was used. No differences were found between zinc deficient and zinc adequate rats in taste preference aversion scores for quinine sulfate in the first three trial periods; however, in the last trial period rats in the zinc sufficient group drank somewhat less water containing quinine sulfate as a percentage of total water consumption than did rats fed the zinc deficient ration. Significantly higher zinc contents of kidney, brain and parotid salivary glands were seen in zinc adequate rats compared to zinc deficient rats at the end of the study. However, liver and tongue zinc levels were lower for both groups at the close of the study than were those of rats sacrificed at the beginning of the study

Suggestions for an adequate risk communication - experiences based on German epidemiological studies on childhood cancer and neighbourhood to nuclear power plants

International Nuclear Information System (INIS)

Kaatsch, P.

2006-01-01

From the example of the German studies on childhood cancer in the vicinity of nuclear power plants general principles for adequate risk communication could be derived. It is particularly important to explain the complexity of the issue to the public in an adequate way, when dealing with topics of such an emotionally loaded nature. Some rules are required, when explaining the nature of risk to the layman, the press, politicians, or scientists from other fields. The main principle is to create a basis of trustfulness, whereupon results can be presented. In this contribution we derive general and proven specific recommendations for adequate risk communication on the basis of experiences made at the German Childhood Cancer Registry. (orig.)

Separation and identification of selenotrisulfides in epithelial cell homogenates by LC-ICP-MS and LC-ESI-MS after incubation with selenite

DEFF Research Database (Denmark)

Gabel-Jensen, Charlotte; Gammelgaard, Bente; Bendahl, Lars

2006-01-01

. The presence of Cys-Se-SG and GS-Se-SG was verified by LC-ESI-MS. Selenotrisulfides were synthesized by reaction of L-cysteine and L-glutathione with sodium selenite. The reaction mixture contained three main products: selenodicysteine (Cys-Se-Cys), selenocysteine glutathione (Cys...

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'. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Diet quality of Italian yogurt consumers: an application of the probability of adequate nutrient intake score (PANDiet).

Science.gov (United States)

Mistura, Lorenza; D'Addezio, Laura; Sette, Stefania; Piccinelli, Raffaela; Turrini, Aida

2016-01-01

The diet quality in yogurt consumers and non-consumers was evaluated by applying the probability of adequate nutrient intake (PANDiet) index to a sample of adults and elderly from the Italian food consumption survey INRAN SCAI 2005-06. Overall, yogurt consumers had a significantly higher mean intake of energy, calcium and percentage of energy from total sugars whereas the mean percentage of energy from total fat, saturated fatty acid and total carbohydrate were significantly (p yogurt consumers than in non-consumers, (60.58 ± 0.33 vs. 58.58 ± 0.19, p yogurt consumers. The items of calcium, potassium and riboflavin showed the major percentage variation between consumers and non-consumers. Yogurt consumers were more likely to have adequate intakes of vitamins and minerals, and a higher quality score of the diet.

A model for determining when an analysis contains sufficient detail to provide adequate NEPA coverage for a proposed action

International Nuclear Information System (INIS)

Eccleston, C.H.

1994-11-01

Neither the National Environmental Policy Act (NEPA) nor its subsequent regulations provide substantive guidance for determining the Level of detail, discussion, and analysis that is sufficient to adequately cover a proposed action. Yet, decisionmakers are routinely confronted with the problem of making such determinations. Experience has shown that no two decisionmakers are Likely to completely agree on the amount of discussion that is sufficient to adequately cover a proposed action. one decisionmaker may determine that a certain Level of analysis is adequate, while another may conclude the exact opposite. Achieving a consensus within the agency and among the public can be problematic. Lacking definitive guidance, decisionmakers and critics alike may point to a universe of potential factors as the basis for defending their claim that an action is or is not adequately covered. Experience indicates that assertions are often based on ambiguous opinions that can be neither proved nor disproved. Lack of definitive guidance slows the decisionmaking process and can result in project delays. Furthermore, it can also Lead to inconsistencies in decisionmaking, inappropriate Levels of NEPA documentation, and increased risk of a project being challenged for inadequate coverage. A more systematic and less subjective approach for making such determinations is obviously needed. A paradigm for reducing the degree of subjectivity inherent in such decisions is presented in the following paper. The model is specifically designed to expedite the decisionmaking process by providing a systematic approach for making these determination. In many cases, agencies may find that using this model can reduce the analysis and size of NEPA documents

Structural comparison of tRNA m1A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions

Directory of Open Access Journals (Sweden)

Guelorget Amandine

2011-12-01

Full Text Available Abstract Background tRNA m1A58 methyltransferases (TrmI catalyze the transfer of a methyl group from S-adenosyl-L-methionine to nitrogen 1 of adenine 58 in the T-loop of tRNAs from all three domains of life. The m1A58 modification has been shown to be essential for cell growth in yeast and for adaptation to high temperatures in thermophilic organisms. These enzymes were shown to be active as tetramers. The crystal structures of five TrmIs from hyperthermophilic archaea and thermophilic or mesophilic bacteria have previously been determined, the optimal growth temperature of these organisms ranging from 37°C to 100°C. All TrmIs are assembled as tetramers formed by dimers of tightly assembled dimers. Results In this study, we present a comparative structural analysis of these TrmIs, which highlights factors that allow them to function over a large range of temperature. The monomers of the five enzymes are structurally highly similar, but the inter-monomer contacts differ strongly. Our analysis shows that bacterial enzymes from thermophilic organisms display additional intermolecular ionic interactions across the dimer interfaces, whereas hyperthermophilic enzymes present additional hydrophobic contacts. Moreover, as an alternative to two bidentate ionic interactions that stabilize the tetrameric interface in all other TrmI proteins, the tetramer of the archaeal P. abyssi enzyme is strengthened by four intersubunit disulfide bridges. Conclusions The availability of crystal structures of TrmIs from mesophilic, thermophilic or hyperthermophilic organisms allows a detailed analysis of the architecture of this protein family. Our structural comparisons provide insight into the different molecular strategies used to achieve the tetrameric organization in order to maintain the enzyme activity under extreme conditions.

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.

The Pedagogical Performance Of The Judge In The Search For A Fair Trial And An Adequate Provision: Judicial Role

Directory of Open Access Journals (Sweden)

Elaine Harzheim Macedo

2017-02-01

Full Text Available This work analyzes the possibility of pedagogical performance of the judge in the search for a fair trial and adequate process. Using deductive methodology, starts with the duties and powers of the judge to assess the possibility of inducing practices based on the good faith by applying bad faith litigation and determination of initial amendment. The judge can be an agent that helps in the implementation of fair trial and adequate provision and should not remain inert in relation to clear violations of fundamental procedural rights. This activity should not generalise situations, being based on the analysis of specific cases.

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.

Do people know adequately about leptospirosis? A knowledge assessment survey in post-outbreak situation in Sri Lanka

Directory of Open Access Journals (Sweden)

Suneth B Agampodi

2010-01-01

Conclusions: Although there is not adequate information on MDD prevalence in some areas of Iran, the overall current preva-lence of MDD in the country is high and females are at the greater risk of disease.

A traumatic central cord syndrome occurring after adequate decompression for cervical spondylosis: biomechanics of injury: case report.

Science.gov (United States)

Dickerman, Rob D; Lefkowitz, Michael; Epstein, Joseph A

2005-10-15

Case report with review of the literature. To present the first case of a central cord syndrome occurring after adequate decompression, and review the mechanics of the cervical spinal cord injury and postoperative biomechanical and anatomic changes occurring after cervical decompressive laminectomy. Cervical spondylosis is a common pathoanatomic occurrence in the elderly population and is thought to be one of the primary causes for a central cord syndrome. Decompressive laminectomy with or without fusion has been a primary treatment for spondylotic disease and is thought to be protective against further injury. To our knowledge, there are no cases of a central cord syndrome occurring after adequate decompression reported in the literature. Case study with extensive review of the literature. The patient underwent C3-C7 cervical laminectomy without complications. After surgery, the patient's spasticity and gait difficulties improved. She was discharged to inpatient rehabilitation for further treatment of upper extremity weakness. The patient fell in the rehabilitation center, with a central cord syndrome despite adequate decompression of her spinal canal. The patient was treated conservatively for the central cord and had minimal improvement. Decompressive laminectomy provides an immediate decompressive effect on the spinal cord as seen by the dorsal migration of the cord, however, the biomechanics of the cervical spine after decompressive laminectomy remain uncertain. This case supports the ongoing research and need for more intensive research on postoperative cervical spine biomechanics, including decompressive laminectomies, decompressive laminectomy and fusion, and laminoplasty.

Does Initial Learning about the Meaning of Fractions Present Similar Challenges for Students with and without Adequate Whole-Number Skill?

Science.gov (United States)

Namkung, Jessica M; Fuchs, Lynn S; Koziol, Natalie

2018-01-01

The purposes of this study were to (a) explore whether early fractions understanding at 4 th grade is differentially challenging for students with versus without adequate whole-number competence and (b) identify specific whole-number skill associated with difficulty in fractions understanding. Based on initial whole-number competence, 1,108 4 th graders were classified as having (a) adequate whole-number competence ( n = 775), (b) less severe whole-number difficulty ( n = 201), and (c) severe whole-number difficulty ( n = 132). At the end of 4 th grade, they were assessed on fractions understanding and further classified as with versus without difficulty in fractions understanding. Multi-level logistic regression indicated that compared to students with adequate whole-number competence, those with less severe whole-number difficulty were almost 5 times as likely to experience difficulty with fractions understanding whereas those with severe whole-number difficulty were about 32 times as likely to experience difficulty with fractions understanding. Students with severe whole-number difficulty were about 7 times as likely to experience difficulty with fractions understanding compared to those with less severe whole-number difficulty. Among students with adequate whole-number competence, the pretest whole-number skill distinguishing those with versus without difficulty in fractions understanding was basic division facts (i.e., 2-digit dividend ÷ 1-digit divisor) and simple multiplication (i.e., 3-digit × 1-digit without regrouping). The role of whole-number competence in developing initial fractions understanding and implications for instruction are discussed.

The yield of adequate and conclusive fine-needle aspiration results in thyroid nodules is uniform across functional and goiter types.

Science.gov (United States)

Liel, Y

1999-01-01

Relatively little is known about the cytological characteristics of hyperfunctioning (hot) thyroid nodules. Concern has been expressed that fine-needle aspiration (FNA) identifies hot nodules as follicular tumors or indeterminate, and as a consequence patients could be unnecessarily referred for surgery. Between 1979 and 1996, thyroid FNA was performed on 829 patients. Result of thyroid scan was available in 326; 69 (21%) patients had hot, and 257 (79%) had warm or cold thyroid nodules. Nodules in each of these major groups were divided into 2 subgroups: clinically solitary nodules and dominant nodules in multinodular goiters (MNG). The frequencies of adequate versus inadequate FNA samples, and of conclusive versus indeterminate FNA results were determined separately for each of the groups and subgroups. In addition, patients with hot nodules and overt hyperthyroidism were identified and evaluated separately. Bivariate analyses were performed for the frequency of adequate versus inadequate smears and conclusive versus indeterminate results between hot, toxic, and cold-warm nodules, and between solitary nodules and MNG. The frequency of adequate aspirations and conclusive results in the various groups and subgroups was found to be statistically indistinguishable. In conclusion, the yield of adequate samples and the rate of conclusive results of FNA in thyroid nodules is similar, irrespective of the functional state or of goiter presentation. Hot thyroid nodules do not seem to produce an increase in the rate of inadequate or indeterminate FNA results, and therefore, do not affect the overall performance of thyroid FNA.

Europe's gas consumption and imports to increase with adequate low cost supplies

International Nuclear Information System (INIS)

Odell, P.R.

1997-01-01

Gas in Europe has always been sold above its long-run supply price. Lower prices, however, still permit profitable indigeneous supply expansion. As further reductions in production and transport costs from technological advances are expected, this will continue based on the exploitation of large proven and probable reserves. By 2025, indigeneous output will be 60% up on 1995. Nevertheless, an average 2.2%/annum growth in gas demand will increase import dependence from 130 to 320 BCM over this period. Future international oil prices indicate gas-equivalent border values adequate to secure profitable supply from a range of external sources, leading to continuing competition for markets and the diversification of imports. (9 tables; 31 references). (author)

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…

Selection of adequate site location during early stages of construction project management: A multi-criteria decision analysis approach

Science.gov (United States)

Marović, Ivan; Hanak, Tomaš

2017-10-01

In the management of construction projects special attention should be given to the planning as the most important phase of decision-making process. Quality decision-making based on adequate and comprehensive collaboration of all involved stakeholders is crucial in project’s early stages. Fundamental reasons for existence of this problem arise from: specific conditions of construction industry (final products are inseparable from the location i.e. location has a strong influence of building design and its structural characteristics as well as technology which will be used during construction), investors’ desires and attitudes, and influence of socioeconomic and environment aspects. Considering all mentioned reasons one can conclude that selection of adequate construction site location for future investment is complex, low structured and multi-criteria problem. To take into account all the dimensions, the proposed model for selection of adequate site location is devised. The model is based on AHP (for designing the decision-making hierarchy) and PROMETHEE (for pairwise comparison of investment locations) methods. As a result of mixing basis feature of both methods, operational synergies can be achieved in multi-criteria decision analysis. Such gives the decision-maker a sense of assurance, knowing that if the procedure proposed by the presented model has been followed, it will lead to a rational decision, carefully and systematically thought out.

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

Maintenance of exercise training benefits is associated with adequate milk and dairy products intake in elderly hypertensive subjects following detraining.

Science.gov (United States)

Moraes, Wilson Max Almeida Monteiro de; Santos, Neucilane Silveira Dos; Aguiar, Larissa Pereira; Sousa, Luís Gustavo Oliveira de

2017-01-01

To investigate whether maintenance of exercise training benefits is associated with adequate milk and dairy products intake in hypertensive elderly subjects after detraining. Twenty-eight elderly hypertensive patients with optimal clinical treatment underwent 16 weeks of multicomponent exercise training program followed by 6 weeks of detraining, and were classified according to milk and dairy products intake as low milk (exercise training, there was a significant reduction (pexercise training benefits related to pressure levels, lower extremity strength and aerobic capacity, is associated with adequate milk and dairy products intake in hypertensive elderly subjects following 6 weeks of detraining.

Substitution of cysteine for a conserved alanine residue in the catalytic center of type II iodothyronine deiodinase alters interaction with reducing cofactor

NARCIS (Netherlands)

W. Klootwijk (Willem); T.J. Visser (Theo); G.G.J.M. Kuiper (George)

2002-01-01

textabstractHuman type II iodothyronine deiodinase (D2) catalyzes the activation of T(4) to T(3). The D2 enzyme, like the type I (D1) and type III (D3) deiodinases, contains a selenocysteine (SeC) residue (residue 133 in D2) in the highly conserved catalytic center. Remarkably, all

TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element.

Directory of Open Access Journals (Sweden)

Thomas Spaller

Full Text Available The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes. We determined that a tagged TRE5-A element (TRE5-Absr integrated at 384 of 405 tRNA genes, suggesting that expansion of the current natural TRE5-A population is not limited by the availability of targets. We further observed that TRE5-Absr targets the ribosomal 5S gene on the multicopy extrachromosomal DNA element that carries the ribosomal RNA genes, indicating that TRE5-A integration may extend to the entire RNA polymerase III (Pol III transcriptome. We determined that both natural TRE5-A and cloned TRE5-Absr retrotranspose to locations on the extrachromosomal rDNA element that contain tRNA gene-typical A/B box promoter motifs without displaying any other tRNA gene context. Based on previous data suggesting that TRE5-A targets tRNA genes by locating Pol III transcription complexes, we propose that A/B box loci reflect Pol III transcription complex assembly sites that possess a function in the biology of the extrachromosomal rDNA element.

Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii

International Nuclear Information System (INIS)

Fukunaga, Ryuya; Ishitani, Ryuichiro; Nureki, Osamu; Yokoyama, Shigeyuki

2004-01-01

The leucyl-tRNA synthetase (LeuRS) from P. horikoshii has been overexpressed in Escherichia coli and purified, and cocrystallizations with each of the tRNA Leu isoacceptors have been attempted. Cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the tRNA Leu isoacceptor with the anticodon CAA was used. All five tRNA Leu isoacceptors from the archaeon Pyrococcus horikoshii have been transcribed in vitro and purified. The leucyl-tRNA synthetase (LeuRS) from P. horikoshii was overexpressed in Escherichia coli and purified, and cocrystallizations with each of the tRNA Leu isoacceptors were attempted. Cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the tRNA Leu isoacceptor with the anticodon CAA was used. Electrophoretic analyses revealed that the crystals contain both LeuRS and tRNA Leu , suggesting that they are LeuRS–tRNA Leu complex crystals. A data set diffracting to 3.3 Å resolution was collected from a single crystal at 100 K. The crystal belongs to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 118.18, b = 120.55, c = 231.13 Å. The asymmetric unit is expected to contain two complexes of LeuRS–tRNA Leu , with a corresponding crystal volume per protein weight of 2.9 Å 3 Da −1 and a solvent content of 57.3%

Human tRNAGly acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 Å resolution

International Nuclear Information System (INIS)

Förster, Charlotte; Szkaradkiewicz, Karol; Perbandt, Markus; Brauer, Arnd B. E.; Borowski, Tordis; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.

2007-01-01

The human tRNA Gly acceptor-stem microhelix was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 1.2 Å. The major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-tRNA synthetase systems (GlyRS; class II aminoacyl-tRNA synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. The differences in the identity elements of the respective tRNA Gly systems are located within the acceptor stem and include the discriminator base U73. In the present work, the human tRNA Gly acceptor-stem microhelix was crystallized in an attempt to analyze the structural features that govern the correct recognition of tRNA Gly by the eukaryotic/archaebacterial-type glycyl-tRNA synthetase. The crystals of the human tRNA Gly acceptor-stem helix belong to the monoclinic space group C2, with unit-cell parameters a = 37.12, b = 37.49, c = 30.38 Å, α = γ = 90, β = 113.02°, and contain one molecule per asymmetric unit. A high-resolution data set was acquired using synchrotron radiation and the data were processed to 1.2 Å resolution

Characterization of the human laminin beta2 chain locus (LAMB2): linkage to a gene containing a nonprocessed, transcribed LAMB2-like pseudogene (LAMB2L) and to the gene encoding glutaminyl tRNA synthetase (QARS)

DEFF Research Database (Denmark)

Durkin, M E; Jäger, A C; Khurana, T S

1999-01-01

The laminin beta2 chain is an important constituent of certain kidney and muscle basement membranes. We have generated a detailed physical map of a 110-kb genomic DNA segment surrounding the human laminin beta2 chain gene (LAMB2) on chromosome 3p21.3-->p21.2, a region paralogous with the chromosome...... 7q22-->q31 region that contains the laminin beta1 chain gene locus (LAMB1). Several CpG islands and a novel polymorphic microsatellite marker (D3S4594) were identified. The 3' end of LAMB2 lies 16 kb from the 5' end of the glutaminyl tRNA synthetase gene (QARS). About 20 kb upstream of LAMB2 we...... found a gene encoding a transcribed, non-processed LAMB2-like pseudogene (LAMB2L). The sequence of 1.75 kb of genomic DNA at the 3' end of LAMB2L was similar to exons 8-12 of the laminin beta2 chain gene. The LAMB2L-LAMB2-QARS cluster lies telomeric to the gene encoding the laminin-binding protein...

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

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

2011-02-01

Full Text Available To study whether subjects with a molecular genetic diagnosis of familial hypercholesterolemia (FH or familial defective apoB-100 (FDB are being adequately treated.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.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.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.

The genetic code – Thawing the 'frozen accident'

Indian Academy of Sciences (India)

Madhu

2006-10-04

Oct 4, 2006 ... The components foremost involved in this process are the. tRNA molecules whose ... that tRNA species with dual identity (capable of being charged by two ... However, the theory has good support, as the CUG codon in ...

Resonance – Journal of Science Education | Indian Academy of ...

Indian Academy of Sciences (India)

Keywords. Chemical synthesis of genes for yeast alanine tRNA and E. coli supressor tRNA; Khorana's philosophy on science. Author Affiliations. Marvin H Caruthers1. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA.

Disease: H01186 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available a disorder associated with an inherited selenocysteine (Sec) incorporation defect, caused by mutations in SECI...eiodinase type 2 (DIO2) enzymatic activity not linked to the DIO2 locus. Inherited metabolic disease SECISBP...C, Boran G, Schomburg L, Weiss RE, Refetoff S ... TITLE ... Mutations in SECISBP2 result in abnormal thyroid h

Bio-fortification and isotopic labelling of Se metabolites in onions and carrots following foliar application of Se and 77Se

DEFF Research Database (Denmark)

Kápolna, Emese; Laursen, Kristian H.; Husted, Søren

2012-01-01

Se. The 77Se- labelled metabolites in onions were predominantly γ-glutamyl-77Se-selenomethyl-selenocysteine (γ-glu-Me77SeCys), 77Se-methylselenocysteine (Me77SeCys) and 77Se-selenomethionine (77SeMet). Furthermore, we report here for the first time the finding in carrots of the bioactive Me77SeCys...

Migration and access to maternal healthcare: determinants of adequate antenatal care and institutional delivery among socio-economically disadvantaged migrants in Delhi, India.

Science.gov (United States)

Kusuma, Yadlapalli S; Kumari, Rita; Kaushal, Sonia

2013-10-01

To identify the determinants of adequate antenatal care (ANC) utilisation and institutional deliveries among socio-economically disadvantaged migrants living in Delhi, India. In a cross-sectional survey, 809 rural-urban migrant mothers with a child aged below 2 years were interviewed with a pretested questionnaire. Data on receiving antenatal, delivery and post-natal services, migration history and other social, demographic and income were collected. Recent migrants used the services significantly less than settled migrants. ANC was adequate only among 37% (35% of recent migrant women and 39% of settled migrants). Multinomial regression revealed that being a recent migrant, multiparous, illiterate and married to an unskilled worker were significant risk factors for receiving inadequate ANC. Around 53% of deliveries took place at home. ANC seeking has a strong influence on place of delivery: 70% of births to women who received inadequate ANC were at home. Women who are educated, had their first delivery after the age of 20 years and received adequate ANC were more likely to deliver their child in hospital. Post-natal care is grossly neglected among these groups. Migrant women, particularly recent migrants, are at the risk of not receiving adequate maternal healthcare. Because migration is a continuing phenomenon, measures to mitigate disadvantage due to migration need to be taken in the healthcare system. © 2013 John Wiley & Sons Ltd.

Brevetoxin-2, is a unique inhibitor of the C-terminal redox center of mammalian thioredoxin reductase-1.

Science.gov (United States)

Chen, Wei; Tuladhar, Anupama; Rolle, Shantelle; Lai, Yanhao; Rodriguez Del Rey, Freddy; Zavala, Cristian E; Liu, Yuan; Rein, Kathleen S

2017-08-15

Karenia brevis, the Florida red tide dinoflagellate produces a suite of neurotoxins known as the brevetoxins. The most abundant of the brevetoxins PbTx-2, was found to inhibit the thioredoxin-thioredoxin reductase system, whereas the PbTx-3 has no effect on this system. On the other hand, PbTx-2 activates the reduction of small disulfides such as 5,5'-dithio-bis-(2-nitrobenzoic acid) by thioredoxin reductase. PbTx-2 has an α, β-unsaturated aldehyde moiety which functions as an efficient electrophile and selenocysteine conjugates are readily formed. PbTx-2 blocks the inhibition of TrxR by the inhibitor curcumin, whereas curcumin blocks PbTx-2 activation of TrxR. It is proposed that the mechanism of inhibition of thioredoxin reduction is via the formation of a Michael adduct between selenocysteine and the α, β-unsaturated aldehyde moiety of PbTx-2. PbTx-2 had no effect on the rates of reactions catalyzed by related enzymes such as glutathione reductase, glutathione peroxidase or glutaredoxin. Copyright © 2017 Elsevier Inc. All rights reserved.

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…

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

Science.gov (United States)

Parlesak, Alexandr; Tetens, Inge; Dejgård Jensen, Jørgen; Smed, Sinne; Gabrijelčič Blenkuš, Mojca; Rayner, Mike; Darmon, Nicole; Robertson, Aileen

2016-01-01

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. 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. 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. Use of linear programming facilitates the generation of low-cost food baskets that are nutritionally adequate, health promoting, and culturally acceptable.

On infrared spectroscopic analysis of transfer RNA secondary structure

Energy Technology Data Exchange (ETDEWEB)

Semenov, M A; Starikov, E B

1987-07-14

Various techniques of IR spectroscopy in the 1550-1750 cm/sup -1/ region employed to analyse the tRNA secondary structure are discussed and a novel improved method is proposed. The main novel features of this method are the approximation of tRNA helical region spectra by catalogue carbonyl absorption bands and approximation of tRNA nonhelical region spectra by those of homopolyribonucleotides. The IR spectra of tRNA/sub yeast//sup phe/ and tRNA/sub E.coli//sup fmet/ in the carbonyl vibration region are explained on the basis of calculated transition moment coupling.

Ribosome•RelA structures reveal the mechanism of stringent response activation

Science.gov (United States)

Loveland, Anna B; Bah, Eugene; Madireddy, Rohini; Zhang, Ying; Brilot, Axel F; Grigorieff, Nikolaus; Korostelev, Andrei A

2016-01-01

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. DOI: http://dx.doi.org/10.7554/eLife.17029.001 PMID:27434674

A Specific Hepatic Transfer RNA for Phosphoserine*

Science.gov (United States)

Mäenpää, Pekka H.; Bernfield, Merton R.

1970-01-01

Radioactive O-phosphoryl-L-serine was detected after alkaline deacylation of rat and rooster liver [3H]seryl-tRNA acylated in vitro with homologous synthetases. Ribonuclease treatment of this tRNA yielded a compound with the properties of phosphoseryl-adenosine. Benzoylated DEAE-cellulose chromatography of seryl-tRNA yielded four distinct peaks, only one of which contained phosphoserine. A unique fraction for phosphoserine was also found on chromatography of nonacylated tRNA. In ribosome binding studies, this fraction responded very slightly with poly(U,C), but not with any of the known serine trinucleotide codons. Substantial incorporation of [3H]-serine into protein from this tRNA species was observed in an aminoacyl-tRNA dependent polysomal system derived from chick oviducts. No phosphoserine was found in Escherichia coli or yeast seryl-tRNA acylated with homologous enzymes, nor in E. coli seryl-tRNA acylated with liver synthetase. In the absence of tRNA, free phosphoserine was not formed in reaction mixtures, which suggests that phosphoseryl-tRNA arises by phosphorylation of the unique seryl-tRNA species. These results demonstrate a discrete tRNASer species in rat and rooster liver containing phosphoserine and suggest that this tRNA is involved in ribosomal polypeptide synthesis. PMID:4943179

Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates.

Science.gov (United States)

Mitra, Sanga; Das, Pijush; Samadder, Arpa; Das, Smarajit; Betai, Rupal; Chakrabarti, Jayprokas

2015-01-01

During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promoter sequences, namely, A-Box and B-Box, were investigated and evidence gathered that the intervention of optional nucleotides at 17a and 17b correlated with the optimal length of the A-Box. The presence of canonical transcription terminator sequences at the immediate vicinity of tRNA genes was ventured. Even though non-canonical introns had been reported in red alga, green alga, and nucleomorph so far, fairly motivating evidence of their existence emerged in tRNA genes of other eukaryotes. Non-canonical introns were seen to interfere with the internal promoters in two cases, questioning their transcription fidelity. In a first of its kind, phylogenetic constructs based on tRNA molecules delineated and built the trees of the vast and diverse invertebrates and vertebrates. Finally, two tRNA models representing the invertebrates and the vertebrates were drawn, by isolating the dominant consensus in the positional fluctuations of nucleotide compositions.

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. Copyright © 2015. Published by Elsevier B.V.

The α-Amino Group of the Threonine Substrate As The General Base During tRNA Aminoacylation: A New Version of Substrate Assisted Catalysis Predicted by Hybrid DFT

Science.gov (United States)

Huang, WenJuan; Bushnell, Eric A. C.; Francklyn, Christopher S.; Gauld, James W.

2013-01-01

Density functional theory-based methods in combination with large chemical models have been used to investigate the mechanism of the second half-reaction catalyzed by Thr-tRNA synthetase; aminoacyl transfer from Thr-AMP onto the A763'OH of the cognate tRNA. In particular, we have examined pathways in which an active site His309 residue is either protonated or neutral (i.e., potentially able to act as a base). In the protonated His309-assisted mechanism, the rate-limiting step is formation of the tetrahedral intermediate. The barrier for this step is 155.0 kJ mol−1 and thus, such a pathway is concluded to not be enzymatically feasible. For the neutral His309-assisted mechanism two models were used with the difference being whether Lys465 was included. For either model the barrier of the rate-limiting step is below the upper-thermodynamic enzymatic limit of ∼125 kJ mol−1. Specifically, without Lys465 the rate-limiting barrier is 122.1 kJ mol−1 and corresponds to a rotation about the tetrahedral intermediates Ccarb—OH bond. For the model with Lys465 the rate-limiting barrier is slightly lower and corresponds to the formation of the tetrahedral intermediate. Importantly, for both neutral His309’ models the neutral amino group of the threonyl substrate directly acts as the proton accepter; in the formation of the tetrahedral intermediate the A763'OH proton is directly transferred onto the Thr-NH2. Therefore, the overall mechanism follows a general substrate assisted catalytic mechanism. PMID:21942566

ENSURING ADEQUATE SAFETY WHEN USING HYDROGEN AS A FUEL

Energy Technology Data Exchange (ETDEWEB)

Coutts, D

2007-01-22

Demonstration projects using hydrogen as a fuel are becoming very common. Often these projects rely on project-specific risk evaluations to support project safety decisions. This is necessary because regulations, codes, and standards (hereafter referred to as standards) are just being developed. This paper will review some of the approaches being used in these evolving standards, and techniques which demonstration projects can implement to bridge the gap between current requirements and stakeholder desires. Many of the evolving standards for hydrogen-fuel use performance-based language, which establishes minimum performance and safety objectives, as compared with prescriptive-based language that prescribes specific design solutions. This is being done for several reasons including: (1) concern that establishing specific design solutions too early will stifle invention, (2) sparse performance data necessary to support selection of design approaches, and (3) a risk-adverse public which is unwilling to accept losses that were incurred in developing previous prescriptive design standards. The evolving standards often contain words such as: ''The manufacturer shall implement the measures and provide the information necessary to minimize the risk of endangering a person's safety or health''. This typically implies that the manufacturer or project manager must produce and document an acceptable level of risk. If accomplished using comprehensive and systematic process the demonstration project risk assessment can ease the transition to widespread commercialization. An approach to adequately evaluate and document the safety risk will be presented.

Hydroxyapatite clay for gap filling and adequate bone ingrowth.

Science.gov (United States)

Maruyama, M; Terayama, K; Ito, M; Takei, T; Kitagawa, E

1995-03-01

In uncemented total hip arthroplasty, a complete filling of the gap between femoral prosthesis and the host bone is difficult and defects would remain, because the anatomy of the reamed intramedullary canal cannot fit the prosthesis. Therefore, it seems practical to fill the gap with a clay containing hydroxyapatite (HA), which has an osteoconductive character. The clay (HA clay) is made by mixing HA granules (size 0.1 mm or more) having a homogeneous pore distribution and a porosity of 35-48 vol%, and a viscous substance such as a saline solution of sodium alginate (SSSA). In the first experiment, the ratio of HA granules and sodium alginate in SSSA is set for the same handling properties of HA clay and polymethylmethacrylate bone cement (standard viscosity) before hardening. As a result, the ratio is set for 55 wt% of HA in the clay and 12.5 wt% of sodium alginate in SSSA (i.e., HA:sodium alginate:saline solution = 9.8:1:7). In the second study, the gap between the femoral stem and bone model is completely filled with HA clay. However, the gap is not filled only with HA granules or HA granules mixed with saline solution. In the third animal experiment, using an unloaded model, histology shows that HA clay has an osteoconductive property bridging the gap between the implant and the cortical bone without any adverse reaction. HA clay is considered a useful biomaterial to fill the gap with adequate bone ingrowth.

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNATyr

Czech Academy of Sciences Publication Activity Database

Lopes, R.R.S.; Silveira, G. de O.; Eitler, R.; Vidal, R.S.; Kessler, A.; Hinger, S.; Paris, Zdeněk; Alfonzo, J. D.; Polycarpo, C.

2016-01-01

Roč. 22, č. 8 (2016), s. 1190-1199 ISSN 1355-8382 R&D Projects: GA ČR GJ15-21450Y Institutional support: RVO:60077344 Keywords : Trypanosoma * tRNA * tRNA editing * splicing * intron Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.605, year: 2016

Choosing an adequate design and analysis in cross-cultural personality research

Directory of Open Access Journals (Sweden)

Jia He

2017-02-01

Full Text Available The flourishing of cross-cultural personality research requires a keen eye for rigorous methodology in such research. With decades of experience in cross-cultural research methods, we have come to appreciate that methodological aspects of such studies are critical for obtaining valid findings. Ill-designed or -conducted studies may produce results that are difficult to interpret. A careful design and analysis can help to deal with various methodological problems in cross-cultural personality studies. Drawing on the extensive knowledge that has been accumulated in cross-cultural and personality research in the past decades, we describe a framework of bias and equivalence that enables the choice of adequate research methods and the avoidance of pitfalls that endanger valid conclusions in cross-cultural personality research. Specifically, we focus on sampling issues, test adaptations, and the combination of emic and etic approaches in this short review article. We encourage researchers to use the tools and experience that are available to considerably enlarge our insights in cross-cultural differences and similarities in personality research.

Human immunodeficiency virus uses tRNA(Lys,3) as primer for reverse transcription in HeLa-CD4+ cells

NARCIS (Netherlands)

Das, A. T.; Koken, S. E.; Essink, B. B.; van Wamel, J. L.; Berkhout, B.

1994-01-01

Significant amounts of different tRNA molecules are present in retroviral particles, but one specific tRNA species functions as primer in reverse transcription. It is generally believed that the HIV-1 virus uses the tRNA(Lys,3) molecule as primer. This is based on sequence complementarity between

Funding an Adequate Education for America's Youth: A Plan for Melding Political and Market Definitions of Educational Adequacy.

Science.gov (United States)

Guthrie, James W.

Noting that American society has conventionally relied on both the political process and the marketplace to arrive at a "definition" of adequate education, but that the political process fails to account for individual preferences while the marketplace can cater to many individual preferences, this paper attempts to combine the two…

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.

Are individual transferable quotas an adequate solution to overfishing and overcapacity? Evidence from Danish fisheries

DEFF Research Database (Denmark)

Merayo Garcia, Eugenia; Nielsen, Rasmus; Hoff, Ayoe

2018-01-01

Individual Transferable Quotas stand in large parts of the fisheries economic literature as the panacea that solves all problems of overfishing and overcapacity of world´s fisheries. However, they are also criticized by a number of authors based on their negative social effects. Individual...... in local fishing communities compared to the national average was found. The Danish experience proves that Individual Transferable Quotas can be an adequate solution with regards to overfishing and overcapacity with also positive effects on the environment due to reduced fuel consumption and fishing...

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.

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

Report: EPA Has Adequate Controls to Manage Advice From Science and Research Federal Advisory Committees, but Transparency Could Be Improved

Science.gov (United States)

Report #17-P-0124, March 13, 2017. Science plays an integral role in the EPA's mission. The EPA has an adequate system of controls to manage recommendations from its science and research federal advisory committees.

Thioacetamide-induced cirrhosis in selenium-adequate mice displays rapid and persistent abnormity of hepatic selenoenzymes which are mute to selenium supplementation

International Nuclear Information System (INIS)

Zhang Jinsong; Wang Huali; Yu Hanqing

2007-01-01

Selenium reduction in cirrhosis is frequently reported. The known beneficial effect of selenium supplementation on cirrhosis is probably obtained from nutritionally selenium-deficient subjects. Whether selenium supplementation truly improves cirrhosis in general needs additional experimental investigation. Thioacetamide was used to induce cirrhosis in selenium-adequate and -deficient mice. Selenoenzyme activity and selenium content were measured and the influence of selenium supplementation was evaluated. In Se-adequate mice, thioacetamide-mediated rapid onset of hepatic oxidative stress resulted in an increase in thioredoxin reductase activity and a decrease in both glutathione peroxidase activity and selenium content. The inverse activity of selenoenzymes (i.e. TrxR activity goes up and GPx activity goes down) was persistent and mute to selenium supplementation during the progress of cirrhosis; accordingly, cirrhosis was not improved by selenium supplementation in any period. On the other hand, selenium supplementation to selenium-deficient mice always more efficiently increased hepatic glutathione peroxidase activity and selenium content compared with those treated with thioacetamide, indicating that thioacetamide impairs the liver bioavailability of selenium. Although thioacetamide profoundly affects hepatic selenium status in selenium-adequate mice, selenium supplementation does not modify the changes. Selenium supplementation to cirrhotic subjects with a background of nutritional selenium deficiency can improve selenium status but cannot restore hepatic glutathione peroxidase and selenium to normal levels

Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNAIle2 and ATP

International Nuclear Information System (INIS)

Osawa, Takuo; Inanaga, Hideko; Kimura, Satoshi; Terasaka, Naohiro; Suzuki, Tsutomu; Numata, Tomoyuki

2011-01-01

A. fulgidus TiaS was cocrystallized with tRNA Ile2 and ATP and X-ray diffraction data were collected to 2.9 Å resolution using a synchrotron-radiation source. The cytidine at the first anticodon position of archaeal tRNA Ile2 , which decodes the isoleucine AUA codon, is modified to 2-agmatinylcytidine (agm 2 C) to guarantee the fidelity of protein biosynthesis. This post-transcriptional modification is catalyzed by tRNA Ile -agm 2 C synthetase (TiaS) using ATP and agmatine as substrates. Archaeoglobus fulgidus TiaS was overexpressed in Escherichia coli cells and purified. tRNA Ile2 was prepared by in vitro transcription with T7 RNA polymerase. TiaS was cocrystallized with both tRNA Ile2 and ATP by the vapour-diffusion method. The crystals of the TiaS–tRNA Ile2 –ATP complex diffracted to 2.9 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the primitive hexagonal space group P3 2 21, with unit-cell parameters a = b = 131.1, c = 86.6 Å. The asymmetric unit is expected to contain one TiaS–tRNA Ile2 –ATP complex, with a Matthews coefficient of 2.8 Å 3 Da −1 and a solvent content of 61%

The T. brucei TRM5 methyltransferase plays an essential role in mitochondrial protein synthesis and function

Czech Academy of Sciences Publication Activity Database

Paris, Z.; Horáková, Eva; Rubio, M.A.T.; Sample, P.; Fleming, I.M.C.; Armocida, S.; Lukeš, Julius; Alfonzo, J. D.

2013-01-01

Roč. 19, č. 5 (2013), s. 649-658 ISSN 1355-8382 R&D Projects: GA ČR(CZ) GAP305/11/2179; GA MŠk LH12104 Institutional support: RVO:60077344 Keywords : Trypanosoma * tRNA * methylation * tRNA import * mitochondrion Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.622, year: 2013

Calcium regulates the expression of a Dictyostelium discoideum ...

Indian Academy of Sciences (India)

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 ...

The Genomic Pattern of tDNA Operon Expression in E. coli.

Directory of Open Access Journals (Sweden)

2005-06-01

Full Text Available In fast-growing microorganisms, a tRNA concentration profile enriched in major isoacceptors selects for the biased usage of cognate codons. This optimizes translational rate for the least mass invested in the translational apparatus. Such translational streamlining is thought to be growth-regulated, but its genetic basis is poorly understood. First, we found in reanalysis of the E. coli tRNA profile that the degree to which it is translationally streamlined is nearly invariant with growth rate. Then, using least squares multiple regression, we partitioned tRNA isoacceptor pools to predicted tDNA operons from the E. coli K12 genome. Co-expression of tDNAs in operons explains the tRNA profile significantly better than tDNA gene dosage alone. Also, operon expression increases significantly with proximity to the origin of replication, oriC, at all growth rates. Genome location explains about 15% of expression variation in a form, at a given growth rate, that is consistent with replication-dependent gene concentration effects. Yet the change in the tRNA profile with growth rate is less than would be expected from such effects. We estimated per-copy expression rates for all tDNA operons that were consistent with independent estimates for rDNA operons. We also found that tDNA operon location, and the location dependence of expression, were significantly different in the leading and lagging strands. The operonic organization and genomic location of tDNA operons are significant factors influencing their expression. Nonrandom patterns of location and strandedness shown by tDNA operons in E. coli suggest that their genomic architecture may be under selection to satisfy physiological demand for tRNA expression at high growth rates.

Recognition of Escherichia coli valine transfer RNA by its cognate synthetase: A fluorine-19 NMR study

International Nuclear Information System (INIS)

Chu, Wenchy; Horowitz, J.

1991-01-01

Interactions of 5-fluorouracil-substituted Escherichia coli tRNA Val with its cognate synthetase have been investigated by fluorine-19 nuclear magnetic resonance. Valyl-tRNA synthetase (VRS) (EC 6.1.1.9), purified to homogeneity from an overproducing strain of E. coli, differs somewhat from VRS previously isolated from E. coli K12. Its amino acid composition and N-terminal sequence agree well with results derived from the sequence of the VRS gene. Apparent K M and V max values of the purified VRS are the same for both normal and 5-fluorouracil (FUra)-substituted tRNA Val . Binding of VRS to (FUra)tRNA Val induces structural perturbations that are reflected in selective changes in the 19 F NMR spectrum of the tRNA. Addition of increasing amounts of VRS results in a gradual loss of intensity at resonances corresponding to FU34, FU7, and FU67, with FU34, at the wobble position of the anticodon, being affected most. At higher VRS/tRNA ratios, a broadening and shifting of FU12 and of FU4 and/or FU8 occur. These results indicate that VRS interacts with tRNA Val along the entire inside of the L-shape molecule, from the acceptor stem to the anticodon. Valyl-tRNA synthetase also causes a splitting of resonances FU55 and FU64 in the T-loop and stem of tRNA Val , suggesting conformational changes in this part of the molecule. No 19 F NMR evidence was found for formation of the Michael adduct between VRS and FU8 of 5-fluorouracil-substituted tRNA Val that has been proposed as a common intermediate in the aminoacylation reaction

Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNALys.

Science.gov (United States)

Sonawane, Kailas D; Kamble, Asmita S; Fandilolu, Prayagraj M

2017-12-27

Deficiency of 5-taurinomethyl-2-thiouridine, τm 5 s 2 U at the 34th 'wobble' position in tRNA Lys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA Lys , recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA Lys in presence and absence of τm 5 s 2 U 34 and N 6 -threonylcarbamoyl adenosine (t 6 A 37 ) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA Lys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm 5 s 2 U 34 and t 6 A 37 with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm 5 s 2 U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA Lys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA Lys with τm 5 s 2 U and t 6 A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm 5 s 2 U and t 6 A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.

Fulltext PDF

Indian Academy of Sciences (India)

2006-10-04

Oct 4, 2006 ... subtlis RNase on the cell-free protein synthesizing system and found that E. coli tRNA ..... methylated guanosine in its place rather than being simply undermodified ... 31(4), October 2006 analysed to date, taking the C3'-endo-anti form which may .... only marginally affected tRNA function or cellular viability.

RNA quality control in yeast - what is good and what is bad?

DEFF Research Database (Denmark)

Andersen, Kasper Røjkjær; Brodersen, Ditlev Egeskov

positions in the tRNA molecules [2]. We believe that in such cases, the tRNAs are recognized by a common structural alteration that causes part of the molecule to unfold and thereby mark the tRNA as defect. We therefore want to isolate and crystallize the RNA binding proteins Air1p or Air2p in complex...... with aberrant tRNA analogous to gain knowledge of how the cell determines which RNAs are good and bad and use this as a model system for how the cell in general recognizes aberrant RNAs. So far, Air1p and Air2p have been cloned from different yeast organisms and the first expression tests of the proteins have...

The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome.

Science.gov (United States)

Hountondji, Codjo; Bulygin, Konstantin; Créchet, Jean-Bernard; Woisard, Anne; Tuffery, Pierre; Nakayama, Jun-Ichi; Frolova, Ludmila; Nierhaus, Knud H; Karpova, Galina; Baouz, Soria

2014-01-01

We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

Entwicklung und Anwendung von Methoden zur Bestimmung von Selen-Spezies in human-biologischem Material

OpenAIRE

Jäger, Thomas

2014-01-01

Selen ist essentieller Bestandteil von mehr als 25 physiologisch wichtigen menschlichen Enzymen. Der tägliche Bedarf wird überwiegend in Form von organischen Selenverbindungen wie Selenmethionin oder Selenocystein aus der Nahrung aufgenommen. Weitere Expositionswege sind die Einnahme von Nahrungsergänzungsmitteln zur Selensupplementation sowie die inhalative oder dermale Aufnahme von in erster Linie anorganischen Selenverbindungen oder elementarem Selen an Arbeitsplätzen der Selen-verarbeiten...

Precise femtosecond laser ablation of dental hard tissue: preliminary investigation on adequate laser parameters

International Nuclear Information System (INIS)

Hikov, Todor; Pecheva, Emilia; Petrov, Todor; Montgomery, Paul; Antoni, Frederic; Leong-Hoi, Audrey

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. (paper)

Evidenced-based, practical food portion sizes for preschool children and how they fit into a well balanced, nutritionally adequate diet.

Science.gov (United States)

More, J A; Emmett, P M

2015-04-01

Healthy eating guidelines for 1-4-year-old children are available but evidence-based portion sizes have not been specified. Parents and early-years providers are concerned about under- or over-feeding young children. The present study aimed to report detailed information about appropriate average portion size ranges and suggest a practical food plan for feeding preschool children, providing adequate nutrient intakes within energy requirements. Two sources of information were used to obtain an appropriate portion size range for the types of foods normally eaten by this age group. Median portions of a variety of foods were combined into a food plan fulfilling healthy eating guidelines regarding the number of servings from each food group. The nutrient and energy content of the plan was assessed and compared with recommended adequate nutrient intakes and percentage energy contributions from macronutrients. UK children, aged 1-4 years, taking part in Avon Longitudinal Study of Parents and Children and National Diet and Nutrition Survey, were used in the present study. Portion size ranges were developed for 164 foods. The theoretical food plan using foods with high to medium nutrient density was shown to provide an adequate intake of all nutrients, except vitamin D, for which there are very few food sources. These practical food portion size ranges could be used both in early years settings and in advice to parents. The food plan emphasises the need to include a variety of nutrient-dense foods if a balanced diet is to be achieved for preschool children. © 2014 The British Dietetic Association Ltd.

Adequate Consultation And Dialogue With Local Community Unlocking The Untapped Potential For Peace And Development Evidences From South Omo Zone

Directory of Open Access Journals (Sweden)

Mohammed Yimer

2017-10-01

Full Text Available The paper argues that adequate consultation and public wide dialogues at the grass root level are the two potential entry points in times of development interventions. This will foster peace among the nearby people and led a foundation for the subsequent development. The study was undertaken to examine whether the agro-pastoral communities of South Omo zone were jeopardized as a result of the Omo Kuraz Sugar development project or not. It also targeted whether there was adequate consultation with the local people at the earliest days of the project. Adopting Ethnographic design the study accompanied by primary data collected through participant observation focus group discussion and key informant interview indicated that there were attempts to consult the indigenous people though not adequate. It also indicated that despite the absence of compensation for the local displaced people due to their mobile life the people were not endangered as a result of the project. This project as a development project that is established at the communal land of the agro-pastoralists is providing training for the nearby people to hire them in its various offices. Far from the claims of the various oversees institutions propounded as if the agro-pastoral communities were miserably suffered from such a project the people consider it as if it is their own project. The study implied that South Omo zone is a counter example of how local level consultation and a wide range of dialogue are indispensable preconditions to foster peace and development in many pastoral and agro-pastoral areas of the country.

Biochemical characterization of the deafness-associated mitochondrial tRNASer(UCN) A7445G mutation in osteosarcoma cell cybrids

International Nuclear Information System (INIS)

Li Xiaoming; Zhang, Linda S.; Fischel-Ghodsian, Nathan; Guan Minxin

2005-01-01

The deafness-associated A7445G mutation in the precursor of mitochondrial tRNA Ser(UCN) has been identified in several pedigrees from different ethnic backgrounds. To determine the role of nuclear background in the biochemical manifestation associated with the A7445G mutation, we performed a biochemical characterization of this mutation using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from a New Zealand family into human osteosarcoma mtDNA-less (ρ 0 ) cells. Compared with three control cybrids, three cybrids derived from an affected matrilineal relative carrying the homoplasmic A7445G mutation exhibited ∼38-57% decrease in the steady-state level of tRNA Ser(UCN) , which is less reduced levels than in lymphoblastoid cells in the previous study. Furthermore, ∼22% reduction in the level of aminoacylation of tRNA Ser(UCN) was observed in the mutant cybrid cells. Interestingly, ∼60-63% decrease of steady-state level of ND6 gene, which belongs to the same precursor as that of tRNA Ser(UCN) , in cybrid cell lines carrying the A7445G mutation, is more than that observed in lymphoblastoid cells. These observations strongly point out a mechanistic link between the processing defect of the tRNA Ser(UCN) precursor and decreased stability of ND6 mRNA precursor. These results also imply the influence of nuclear background on the biochemical phenotype associated with the A7445G mutation

Studies of interactions of porphyrins with transfer RNA by high-resolution NMR

International Nuclear Information System (INIS)

Birdsall, W.J.; Lehigh Univ., Bethlehem, PA; Anderson, W.R. Jr; Foster, N.

1989-01-01

The interactions of tetra-4N-methulpyridyl porphyrin and its zinc (II), copper (II) and manganese (III) complexes with brewer's yeast type V phenylalanine specific tRNA have been evaluated by high-resolution NMR. Differences in chemical shifts have been noted for thre proton resonances in response to the presence of small quantities of the fre base and the zinc and copper complexes. The protons giving rise to these signals are located on bases T54 and psi55, both of which are involved in the primary intraloop and interloop hydroen bonds that hold the D and TpsiC loops together in the tertiary structure. In addition, broadening of specific resonances due to hydrogen bonding protons in the D stem at low ratios of porphyrin to tRNA indicates that the association of porphyrins increases the rate of imino proton exchange. The titration of the tRNA with the manganese (III) complex did not eveal shifts or spcific broadening comparable to the other porpyrins at low ratios. The changes induced in the NMR spectrum of tNA by porphyrins define their site of interaction with the polynucleotide. This site, at the outside of the elbow-bend in the tRNA 'L', is different from the locus of binding in tRNA for other classical DNA intercalators. Furthermore, a new mode of binding may be involved that is neither intercalative nor simply electrostatic. (author). 36 refs.; 4 figs

Monitoring the eye lens: which dose quantity is adequate?

International Nuclear Information System (INIS)

Behrens, R; Dietze, G

2010-01-01

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 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 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 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 p (3) on a slab phantom should be used. As an alternative, dosemeters calibrated in terms of H 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.

Adequate irradiation of the internal jugular lymph node chain: technical considerations

International Nuclear Information System (INIS)

Aref, Amr; Gross, Martin; Fontanesi, James; Devi, Syamala; Kopel, Christine; Thornton, Dale

1997-01-01

Purpose: This research aimed to study the anatomic relationship between the internal jugular vein with the surrounding internal jugular lymph node chain and the underlying bony anatomical structures which are commonly used as landmarks for radiation therapy planning. Methods and Materials: Twelve patients with carcinoma of the head and neck region were studied prospectively. Using our three-dimensional planning system, a beam's-eye view of the internal jugular vein was projected onto a lateral and anterior simulation film. Quantitative measurements were made in every case of the anatomic relationship between the internal jugular vein and the posterior border of the cervical vertebrae and sagittal midline. Results: The distance between the posterior border of the internal jugular vein and the posterior border of the cervical vertebrae ranged between 0 and 2.5 cm. The distances between the sagittal midline and the medial border of the internal jugular veins ranged between 2 and 4 cm. Conclusion: To ensure adequate irradiation of the internal jugular lymph nodes, the posterior border of the lateral radiation therapy upper-neck fields should be placed at least 1 cm posterior to the posterior aspect of the cervical vertebrae. The midline block used in the lower neck anterior field should not exceed 2 cm in width

Are breast biopsies adequately funded? A process cost and revenue analysis

International Nuclear Information System (INIS)

Hahn, M.; Fischbach, E.; Fehm, T.

2011-01-01

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.)

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

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. PMID:24358347

21 CFR 1.283 - What happens to food that is imported or offered for import without adequate prior notice?

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false What happens to food that is imported or offered for import without adequate prior notice? 1.283 Section 1.283 Food and Drugs FOOD AND DRUG... Imported Food Consequences § 1.283 What happens to food that is imported or offered for import without...

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

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

Directory of Open Access Journals (Sweden)

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

Transfer of primer binding site-mutated simian immunodeficiency virus vectors by genetically engineered artificial and hybrid tRNA-like primers

DEFF Research Database (Denmark)

Hansen, A C; Grunwald, T; Lund, Anders Henrik

2001-01-01

could be obtained by cotransfection of a gene for an engineered tRNA(Pro)-tRNA hybrid with a match to PBS-Pro. The importance of tRNA backbone identity was further analyzed by complementing the PBS-X2 vector with a gene for a matching x2 primer with a tRNA backbone, which led to three- to fourfold...

Superposition of two tRNASer acceptor stem crystal structures: Comparison of structure, ligands and hydration

International Nuclear Information System (INIS)

Eichert, Andre; Fuerste, Jens P.; Ulrich, Alexander; Betzel, Christian; Erdmann, Volker A.; Foerster, Charlotte

2010-01-01

We solved the X-ray structures of two Escherichia coli tRNA Ser acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA Ser microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to the surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.

tRNAs: cellular barcodes for amino acids

DEFF Research Database (Denmark)

Banerjee, Rajat; Chen, Shawn; Dare, Kiley

2010-01-01

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has...... also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond...... translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis....

Adequately Addressing Pediatric Obesity: Challenges Faced by Primary Care Providers.

Science.gov (United States)

Shreve, Marilou; Scott, Allison; Vowell Johnson, Kelly

2017-07-01

To assess the challenges primary care providers encounter when providing counseling for pediatric patients identified as obese. A survey assessed the current challenges and barriers to the screening and treatment of pediatric obesity for providers in northwest Arkansas who provide care to families. The survey consisted of 15 Likert scale questions and 4 open-ended questions. Time, resources, comfort, and cultural issues were reported by providers as the biggest barriers in screening and the treatment of pediatric obesity. All providers reported lack of time as a barrier to providing the care needed for obese children. Cultural barriers of both the provider and client were identified as factors, which negatively affect the care and treatment of obese children. Primary care providers continue to experience challenges when addressing pediatric obesity. In this study, a lack of adequate time to address obesity was identified as the most significant current barrier and may likely be tied to physician resources. Although reimbursement for obesity is increasing, the level of reimbursement does not support the time or the resources needed to treat patients. Many providers reported their patients' cultural view of obesity influenced how they counsel their patients. Increasing providers' knowledge concerning differences in how weight is viewed or valued may assist them in the assessment and care of obese pediatric patients. The challenges identified in previous research continue to limit providers when addressing obesity. Although progress has been made regarding knowledge of guidelines, continuing effort is needed to tackle the remaining challenges. This will allow for earlier identification and intervention, resulting in improved outcomes in pediatric obesity.

Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders

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Andrea Bednářová

2017-05-01

Full Text Available Transfer RNAs (tRNAs are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon–codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.

Metabolism of tRNAs in growing cells of Escherichia coli illuminated with near-ultraviolet light

International Nuclear Information System (INIS)

Hajnsdorf, E.; Favre, A.

1986-01-01

The tRNA metabolism which accompanies illumination of growing E. coli cells has been examined in conditions that led to growth delay. The in vivo formation of the 8-13 link was followed by a fluorimetric procedure and revealed pseudo-first order kinetics very close to those obtained in vitro under the same illumination conditions. Comparison of these kinetics with published radiochromatographic data suggests the transient formation during illumination of a new RNase-T 2 -resistant dinucleotide in tRNA distinct from the 8-13 link. Under illumination some tRNA molecules lack one or more bases in a specific position in the sequence. During the growth lag, uracil incorporation into nucleic acids occurs at between 4-8% of the rate normally observed during exponential growth. However, the pyrimidine ribonucleoside triphosphate pools are strongly perturbed after illumination. Comparison of exogenous [ 3 H]uracil incorporation into two strains proficient or deficient in uracil biosynthesis suggests a derepression of the endogenous path after light treatment. In addition, the UTP-to-CTP conversion is inhibited. In spite of preferential incorporation of exogenously labelled uracil in tRNA after illumination, a possible pyrimidine base turnover cannot be proved. (author)

Influence of different genotypes in the pattern of selenoprotein expression in response to Brazil nut supplementation

OpenAIRE

Janaina Lombello Santos Donadio

2016-01-01

The micronutrient selenium is essential to human physiology. As the amino acid selenocysteine, it is inserted into selenoproteins with a wide range of functions including antioxidant capacity, thyroid hormone metabolism, improvement of immune system, brain function, fertility and reproduction. Low selenium status has been associated with increased risk for chronic diseases, such as cancer, type-2 diabetes and cardiovascular disease. In this context, several studies have been conducted in orde...

Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes

OpenAIRE

Chapple, Charles E.; Guigó, Roderic

2008-01-01

BACKGROUND: Selenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging this assumption, recent comparative analyses of insect genomes have revealed that some insect genomes appear to have lost selenoprotein genes. METHODOLOGY/PRINCIPAL FINDINGS: In this paper we investiga...

Dietary vitamin A intakes of Filipino elders with adequate or low liver vitamin A concentrations as assessed by the deuterated-retinol-dilution method: implications for dietary requirements.

Science.gov (United States)

Ribaya-Mercado, Judy D; Solon, Florentino S; Fermin, Liza S; Perfecto, Christine S; Solon, Juan Antonio A; Dolnikowski, Gregory G; Russell, Robert M

2004-04-01

The vitamin A requirements of elderly humans have not been studied. In a cross-sectional study of 60-88-y-old men (n = 31) and women (n = 31) in rural Philippines, we assessed the dietary intakes of elders with adequate (> or = 0.07 micromol/g) or low (value for elders. The mean (+/- SD) vitamin A intakes of the men and women with adequate vitamin A in liver were 135 +/- 86 and 134 +/- 104 microg retinol activity equivalents (RAE)/d, respectively; intakes of the men and women with low vitamin A in liver were 75 +/- 53 and 60 +/- 27 microg RAE/d, respectively. Total-body vitamin A or liver vitamin A but not serum retinol correlated with dietary RAE, preformed vitamin A, beta-carotene, fat, and protein. An estimated acceptable or sufficient dietary vitamin A intake associated with adequate liver vitamin A concentrations in elders is 6.45 microg RAE/kg body wt; for a reference 76-kg man and a 61-kg woman, these values are approximately 500 and 400 microg RAE/d, respectively. The dietary vitamin A intakes of elders with adequate or low liver vitamin A concentrations as estimated by use of the deuterated-retinol-dilution technique are useful for assessing vitamin A requirements.

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.

Serum albumin-adjusted glycated albumin is an adequate indicator of glycemic control in patients with Cushing's syndrome.

Science.gov (United States)

Kitamura, Tetsuhiro; Otsuki, Michio; Tamada, Daisuke; Tabuchi, Yukiko; Mukai, Kosuke; Morita, Shinya; Kasayama, Soji; Bando, Yukihiro; Shimomura, Iichiro; Koga, Masafumi

2014-12-01

We recently reported that glycated albumin (GA) in patients with Cushing's syndrome is low. In the present study, we examined whether serum albumin (SA)-adjusted GA (SAaGA) is an adequate indicator of glycemic control in patients with Cushing's syndrome. We studied 26 patients with Cushing's syndrome (13 patients without diabetes and 13 patients with diabetes). Twenty six non-diabetic subjects and 26 patients with type 2 diabetes mellitus matched for age, sex and BMI were used as the controls. SAaGA was calculated using the regression formula between SA and GA in non-diabetic patients with Cushing's syndrome and non-diabetic subjects. SA showed a significant correlation with GA in non-diabetic patients with Cushing's syndrome and non-diabetic subjects. GA, but not SAaGA, in non-diabetic patients with Cushing's syndrome was significantly lower than that in the non-diabetic controls. Furthermore, the GA/HbA1c ratio, but not the SAaGA/HbA1c ratio, in diabetic patients with Cushing's syndrome was significantly lower than that in the diabetic controls. The measured GA in the patients with Cushing's syndrome was significantly lower than the estimated GA, but there was no difference between SAaGA and the estimated GA. The present findings suggest that SAaGA is an adequate indicator of the glycemic control in patients with Cushing's syndrome. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily.

Directory of Open Access Journals (Sweden)

Miguel López-Estepa

Full Text Available Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct(6A is a non-thiolated hypermodification found in transfer RNAs (tRNAs in bacteria, protists, fungi and plants. In bacteria and yeast cells ct(6A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct(6A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct(6A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct(6A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.

Are forestation, bio-char and landfilled biomass adequate offsets for the climate effects of burning fossil fuels?

International Nuclear Information System (INIS)

Reijnders, L.

2009-01-01

Forestation and landfilling purpose-grown biomass are not adequate offsets for the CO 2 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 landfilled biomass, but there are major uncertainties about net greenhouse gas emissions linked to the bio-char life cycle, which necessitate suspension of judgement about the adequacy of bio-char addition to soils as an offset for CO 2 emissions from burning fossil fuels.

When one is not enough: prevalence and characteristics of homes not adequately protected by smoke alarms.

Science.gov (United States)

Peek-Asa, C; Allareddy, V; Yang, J; Taylor, C; Lundell, J; Zwerling, C

2005-12-01

The National Fire Protection Association (NFPA) has specific recommendations about the number, location, and type of smoke alarms that are needed to provide maximum protection for a household. No previous studies have examined whether or not homes are completely protected according to these guidelines. The authors describe the prevalence and home characteristics associated with compliance to recommendations for smoke alarm installation by the NFPA. Data are from the baseline on-site survey of a randomized trial to measure smoke alarm effectiveness. The trial was housed in a longitudinal cohort study in a rural Iowa county. Of 1005 homes invited, 691 (68.8%) participated. Information about smoke alarm type, placement, and function, as well as home and occupant characteristics, was collected through an on-site household survey. Although 86.0% of homes had at least one smoke alarm, only 22.3% of homes (approximately one in five) were adequately protected according to NFPA guidelines. Fourteen percent of homes had no functioning smoke alarms. More than half of the homes with smoke alarms did not have enough of them or had installed them incorrectly, and 42.4% of homes with alarms had at least one alarm that did not operate. Homes with at least one high school graduate were nearly four times more likely to be fully protected. Homes that had multiple levels, a basement, or were cluttered or poorly cleaned were significantly less likely to be fully protected. These findings indicate that consumers may not be knowledgeable about the number of alarms they need or how to properly install them. Occupants are also not adequately maintaining the alarms that are installed.

tRNA--the golden standard in molecular biology.

Science.gov (United States)

Barciszewska, Mirosława Z; Perrigue, Patrick M; Barciszewski, Jan

2016-01-01

Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.

Selenium-regulated hierarchy of human selenoproteome in cancerous and immortalized cells lines.

Science.gov (United States)

Touat-Hamici, Zahia; Bulteau, Anne-Laure; Bianga, Juliusz; Jean-Jacques, Hélène; Szpunar, Joanna; Lobinski, Ryszard; Chavatte, Laurent

2018-04-13

Selenoproteins (25 genes in human) co-translationally incorporate selenocysteine using a UGA codon, normally used as a stop signal. The human selenoproteome is primarily regulated by selenium bioavailability with a tissue-specific hierarchy. We investigated the hierarchy of selenoprotein expression in response to selenium concentration variation in four cell lines originating from kidney (HEK293, immortalized), prostate (LNCaP, cancer), skin (HaCaT, immortalized) and liver (HepG2, cancer), using complementary analytical methods. We performed (i) enzymatic activity, (ii) RT-qPCR, (iii) immuno-detection, (iv) selenium-specific mass spectrometric detection after non-radioactive 76 Se labeling of selenoproteins, and (v) luciferase-based reporter constructs in various cell extracts. We characterized cell-line specific alterations of the selenoproteome in response to selenium variation that, in most of the cases, resulted from a translational control of gene expression. We established that UGA-selenocysteine recoding efficiency, which depends on the nature of the SECIS element, dictates the response to selenium variation. We characterized that selenoprotein hierarchy is cell-line specific with conserved features. This analysis should be done prior to any experiments in a novel cell line. We reported a strategy based on complementary methods to evaluate selenoproteome regulation in human cells in culture. Copyright © 2018 Elsevier B.V. All rights reserved.

Thioredoxin Cross-Linking by Nitrogen Mustard in Lung Epithelial Cells: Formation of Multimeric Thioredoxin/Thioredoxin Reductase Complexes and Inhibition of Disulfide Reduction

OpenAIRE

Jan, Yi-Hua; Heck, Diane E.; Casillas, Robert P.; Laskin, Debra L.; Laskin, Jeffrey D.

2015-01-01

The thioredoxin (Trx) system, which consists of Trx and thioredoxin reductase (TrxR), is a major cellular disulfide reduction system important in antioxidant defense. TrxR is a target of mechlorethamine (methylbis(2-chloroethyl)amine; HN2), a bifunctional alkylating agent that covalently binds to selenocysteine/cysteine residues in the redox centers of the enzyme, leading to inactivation and toxicity. Mammalian Trx contains two catalytic cysteines; herein, we determined if HN2 also targets Tr...

Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media

International Nuclear Information System (INIS)

Latham, Michael P.; Hanson, Paul; Brown, Darin J.; Pardi, Arthur

2008-01-01

Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNA Val that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which do not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNA Val was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNA Val . Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for the two helical domains in tRNA Val

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

DEFF Research Database (Denmark)

Parlesak, A.; Tetens, Inge; Dejgård Jensen, Jørgen

2016-01-01

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. 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...... in each of the resulting five baskets was increased through limiting the relative share of individual foods. 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...

Selenium Homeostasis and Clustering of Cardiovascular Risk Factors: A Systematic Review.

Science.gov (United States)

Gharipour, Mojgan; Sadeghi, Masoumeh; Behmanesh, Mehrdad; Salehi, Mansour; Nezafati, Pouya; Gharpour, Amin

2017-10-23

  Selenium is a trace element required for a range of cellular functions. It is widely used for the biosynthesis of the unique amino acid selenocysteine [Sec], which is a structural element of selenoproteins. This systematic review focused on the possible relation between selenium and metabolic risk factors. The literature was searched via PubMed, Scopus, ISI Web of Science, and Google Scholar. Searches were not restricted by time or language. Relevant studies were selected in three phases. After an initial quality assessment, two reviewers extracted all the relevant data, whereas the third reviewer checked their extracted data. All evidence came from experimental and laboratory studies. Selenoprotein P is the best indicator for selenium nutritional levels. In addition, high levels of selenium may increase the risk of metabolic syndrome while the lack of sufficient selenium may also promote metabolic syndrome. selenium supplementation in subjects with sufficient serum selenium levels has a contrary effect on blood pressure, LDL, and total cholesterol. According to the bioavailability of different types of selenium supplementation such as selenomethionine, selenite and selenium-yeast, it seems that the best nutritional type of selenium is selenium-yeast. Regarding obtained results of longitudinal studies and randomized controlled trials, selenium supplementation should not be recommended for primary or secondary cardio-metabolic risk prevention in populations with adequate selenium status.

Stool consistency and stool frequency are excellent clinical markers for adequate colon preparation after polyethylene glycol 3350 cleansing protocol: a prospective clinical study in children.

Science.gov (United States)

Safder, Shaista; Demintieva, Yulia; Rewalt, Mary; Elitsur, Yoram

2008-12-01

Colon preparation for a colonoscopy in children is a difficult task because of the unpalatable taste and large volume of cleansing solution that needs to be consumed to ensure a clean colon. Consequently, an unprepared colon frequently occurs in routine practices, which causes early termination and a repeated procedure. (1) To assess the effectiveness of polyethylene glycol solution (PEG 3350) in preparing the colon of children scheduled for a colonoscopy and (2) to investigate clinical markers associated with an adequate colon preparation before a colonoscopy. A total of 167 children scheduled for a colonoscopy. In a prospective study, children scheduled for a colonoscopy were given PEG 3350 solution (1.5 g/kg per day, up to 100 g/d) over a 4-day preparation period. Each day, a simple questionnaire that documents the amount of liquid consumed, adverse effects, and the number and consistency of stool was completed by the parents. After a colonoscopy procedure, the colon preparation was assigned a number grade. The data were later assessed and were compared to determine the association between the grade of cleansing and the frequency and/or consistency of stool during preparation. Colon preparation was completed in 149 children, 133 of whom were adequately prepared. Inadequate preparation was found in 16 children; the procedure was terminated prematurely in 2 of these patients because of unacceptable conditions. No significant adverse effects were noted. A number of >or=5 stools/d, and liquid stool consistency in the last 2 days of preparation were associated with adequate colon preparation. PEG 3350 solution is safe, efficacious, and tolerable for children. Stool frequency and consistency in the last 2 days of preparation were excellent markers (positive predictive value 91%-95%), which predict an adequately clean colon before a colonoscopy in children.

Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif

OpenAIRE

Shchedrina, Valentina A.; Novoselov, Sergey V.; Malinouski, Mikalai Yu.; Gladyshev, Vadim N.

2007-01-01

Selenocysteine (Sec, U) insertion into proteins is directed by translational recoding of specific UGA codons located upstream of a stem-loop structure known as Sec insertion sequence (SECIS) element. Selenoproteins with known functions are oxidoreductases containing a single redox-active Sec in their active sites. In this work, we identified a family of selenoproteins, designated SelL, containing two Sec separated by two other residues to form a UxxU motif. SelL proteins show an unusual occur...

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.

Complete mitochondrial genome of Skylark, Alauda arvensis (Aves: Passeriformes): the first representative of the family Alaudidae with two extensive heteroplasmic control regions.

Science.gov (United States)

Qian, Chaoju; Wang, Yuanxiu; Guo, Zhichun; Yang, Jianke; Kan, Xianzhao

2013-06-01

The circular mitochondrial genome of Alauda arvensis is 17,018 bp in length, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and 2 extensive heteroplasmic control regions. All of the genes encoded on the H-strand, with the exceptions of one PCG (nad6) and eight tRNA genes (tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser(UCN)), tRNA(Pro), and tRNA(Glu)), as found in other birds' mitochondrial genomes. All of these PCGs are initiated with ATG, while stopped by six types of stop codons. All tRNA genes have the potential to fold into typical clover-leaf structure. Two extensive heteroplasmic control regions were found, and more interestingly, a minisatellite of 37 nucleotides (5'-TCAATCCCATTGATTTCATTATATTAGTATAAAGAAA-3') with 6 tandem repeats was detected at the end of CR2.

Adrenal insufficiency in a child with MELAS syndrome.

Science.gov (United States)

Afroze, Bushra; Amjad, Nida; Ibrahim, Shahnaz H; Humayun, Khadija Nuzhat; Yakob, Yusnita

2014-11-01

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) are established subgroups of mitochondrial encephalomyopathy. m.3243A>G a common point mutation is detected in tRNA in majority of patients with MELAS phenotype whereas m.8344A>G point mutation in tRNA is observed, in MERRF phenotype. Adrenal insufficiency has not been reported in mitochondrial disease, except in Kearns-Sayre Syndrome (KSS), which is a mitochondrial deletion syndrome. We report an unusual presentation in a five year old boy who presented with clinical phenotype of MELAS and was found to have m.8344A>G mutation in tRNA. Addison disease was identified due to hyperpigmentation of lips and gums present from early childhood. This is the first report describing adrenal insufficiency in a child with MELAS phenotype. Copyright © 2014 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

A network of hydrophobic residues impeding helix alphaC rotation maintains latency of kinase Gcn2, which phosphorylates the alpha subunit of translation initiation factor 2.

Science.gov (United States)

Gárriz, Andrés; Qiu, Hongfang; Dey, Madhusudan; Seo, Eun-Joo; Dever, Thomas E; Hinnebusch, Alan G

2009-03-01

Kinase Gcn2 is activated by amino acid starvation and downregulates translation initiation by phosphorylating the alpha subunit of translation initiation factor 2 (eIF2alpha). The Gcn2 kinase domain (KD) is inert and must be activated by tRNA binding to the adjacent regulatory domain. Previous work indicated that Saccharomyces cerevisiae Gcn2 latency results from inflexibility of the hinge connecting the N and C lobes and a partially obstructed ATP-binding site in the KD. Here, we provide strong evidence that a network of hydrophobic interactions centered on Leu-856 also promotes latency by constraining helix alphaC rotation in the KD in a manner relieved during amino acid starvation by tRNA binding and autophosphorylation of Thr-882 in the activation loop. Thus, we show that mutationally disrupting the hydrophobic network in various ways constitutively activates eIF2alpha phosphorylation in vivo and bypasses the requirement for a key tRNA binding motif (m2) and Thr-882 in Gcn2. In particular, replacing Leu-856 with any nonhydrophobic residue activates Gcn2, while substitutions with various hydrophobic residues maintain kinase latency. We further provide strong evidence that parallel, back-to-back dimerization of the KD is a step on the Gcn2 activation pathway promoted by tRNA binding and autophosphorylation. Remarkably, mutations that disrupt the L856 hydrophobic network or enhance hinge flexibility eliminate the need for the conserved salt bridge at the parallel dimer interface, implying that KD dimerization facilitates the reorientation of alphaC and remodeling of the active site for enhanced ATP binding and catalysis. We propose that hinge remodeling, parallel dimerization, and reorientation of alphaC are mutually reinforcing conformational transitions stimulated by tRNA binding and secured by the ensuing autophosphorylation of T882 for stable kinase activation.

The structure of an E. coli tRNAfMet A1-U72 variant shows an unusual conformation of the A1-U72 base pair.

Science.gov (United States)

Monestier, Auriane; Aleksandrov, Alexey; Coureux, Pierre-Damien; Panvert, Michel; Mechulam, Yves; Schmitt, Emmanuelle

2017-05-01

Translation initiation in eukaryotes and archaea involves a methionylated initiator tRNA delivered to the ribosome in a ternary complex with e/aIF2 and GTP. Eukaryotic and archaeal initiator tRNAs contain a highly conserved A 1 -U 72 base pair at the top of the acceptor stem. The importance of this base pair to discriminate initiator tRNAs from elongator tRNAs has been established previously using genetics and biochemistry. However, no structural data illustrating how the A 1 -U 72 base pair participates in the accurate selection of the initiator tRNAs by the translation initiation systems are available. Here, we describe the crystal structure of a mutant E. coli initiator tRNA f Met A 1 -U 72 , aminoacylated with methionine, in which the C 1 :A 72 mismatch at the end of the tRNA acceptor stem has been changed to an A 1 -U 72 base pair. Sequence alignments show that the mutant E. coli tRNA is a good mimic of archaeal initiator tRNAs. The crystal structure, determined at 2.8 Å resolution, shows that the A 1 -U 72 pair adopts an unusual arrangement. A 1 is in a syn conformation and forms a single H-bond interaction with U 72 This interaction requires protonation of the N1 atom of A 1 Moreover, the 5' phosphoryl group folds back into the major groove of the acceptor stem and interacts with the N7 atom of G 2 A possible role of this unusual geometry of the A 1 -U 72 pair in the recognition of the initiator tRNA by its partners during eukaryotic and archaeal translation initiation is discussed. © 2017 Monestier et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A thirty million year-old inherited heteroplasmy.

Directory of Open Access Journals (Sweden)

Vincent Doublet

Full Text Available Due to essentially maternal inheritance and a bottleneck effect during early oogenesis, newly arising mitochondrial DNA (mtDNA mutations segregate rapidly in metazoan female germlines. Consequently, heteroplasmy (i.e. the mixture of mtDNA genotypes within an organism is generally resolved to homoplasmy within a few generations. Here, we report an exceptional transpecific heteroplasmy (predicting an alanine/valine alloacceptor tRNA change that has been stably inherited in oniscid crustaceans for at least thirty million years. Our results suggest that this heteroplasmy is stably transmitted across generations because it occurs within mitochondria and therefore escapes the mtDNA bottleneck that usually erases heteroplasmy. Consistently, at least two oniscid species possess an atypical trimeric mitochondrial genome, which provides an adequate substrate for the emergence of a constitutive intra-mitochondrial heteroplasmy. Persistence of a mitochondrial polymorphism on such a deep evolutionary timescale suggests that balancing selection may be shaping mitochondrial sequence evolution in oniscid crustaceans.

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…

Are we telling the diabetic patients adequately about foot care

International Nuclear Information System (INIS)

Ali, R.; Din, M.J.U.; Jadoon, R.J.; Farooq, U.; Alam, M.A.; Qureshi, A.; Shah, S.U.

2016-01-01

Background: Diabetes mellitus affects more than 285 million people worldwide. The prevalence is expected to rise to 439 million by the year 2030. Diabetic foot ulcers precede 84 percentage of non-traumatic amputations in diabetics. One lower limb is lost every 30 seconds around the world because of diabetic foot ulceration. Apart from being lengthy, the treatment of diabetic foot is also very expensive. There is very limited emphasis on foot care in diabetic patients. Even in developed countries patients feel that they do not have adequate knowledge about foot care. This study was conducted to find out how much information is imparted by doctors to diabetic patients about foot care. Methods: This cross-sectional study was conducted in admitted patients of the Department of Medicine, DHQ Hospital, Abbottabad from May 2014 to June 2015. 139 diabetic patients more than 25 years of age were included by non-probability consecutive sampling. Results: The mean age was 57.17 ( percentage 11.1) years. 35.3 percentage of patients were male and 64.7 percentage were female. The mean duration of diabetes in patients was 8.3 (±6) years. Only 36.7 percentage of patients said that their doctor told them about foot care. Less than 40 percentage of patients knew that they should daily inspect their feet, wash them with gentle warm water, and dry them afterwards. Only 25.2 percentage of the participants knew how to manage corns or calluses on feet. 66.5 percentage of patients knew that they should not walk bare foot. Overall, 63 percentage of our patients had less than 50 percentage knowledge of the 11 points regarding foot care that the investigators asked them. Conclusion: Diabetic foot problems are the one of the costliest, most disabling and disheartening complication of diabetes mellitus. Doctors are not properly telling diabetic patients about foot care. There is a deficiency of knowledge among the diabetic patients regarding foot care. (author)

Mutational analysis of the mitochondrial 12S rRNA and tRNASer(UCN) genes in Tunisian patients with nonsyndromic hearing loss

International Nuclear Information System (INIS)

Mkaouar-Rebai, Emna; Tlili, Abdelaziz; Masmoudi, Saber; Louhichi, Nacim; Charfeddine, Ilhem; Amor, Mohamed Ben; Lahmar, Imed; Driss, Nabil; Drira, Mohamed; Ayadi, Hammadi; Fakhfakh, Faiza

2006-01-01

We explored the mitochondrial 12S rRNA and the tRNA Ser(UCN) genes in 100 Tunisian families affected with NSHL and in 100 control individuals. We identified the mitochondrial A1555G mutation in one out of these 100 families and not in the 100 control individuals. Members of this family harbouring the A1555G mutation showed phenotypic heterogeneity which could be explained by an eventual nuclear-mitochondrial interaction. So, we have screened three nuclear genes: GJB2, GJB3, and GJB6 but we have not found correlation between the phenotypic heterogeneity and variants detected in these genes. We explored also the entire mitochondrial 12S rRNA and the tRNA Ser(UCN) genes. We detected five novel polymorphisms: T742C, T794A, A813G, C868T, and C954T, and 12 known polymorphisms in the mitochondrial 12S rRNA gene. None of the 100 families or the 100 controls were found to carry mutations in the tRNA Ser(UCN) gene. We report here First mutational screening of the mitochondrial 12S rRNA and the tRNA Ser(UCN) genes in the Tunisian population which describes the second family harbouring the A1555G mutation in Africa and reveals novel polymorphisms in the mitochondrial 12S rRNA gene

Strongly anisotropic thermal conductivity and adequate breathability of bilayered films for heat management of on-skin electronics

Science.gov (United States)

Zhou, Tianle; Wei, Hao; Tan, Huaping; Wang, Xin; Zeng, Haibo; Liu, Xiaoheng; Nagao, Shijo; Koga, Hirotaka; Nogi, Masaya; Sugahara, Tohru; Suganuma, Katsuaki

2018-07-01

Thin-film wearable electronics are required to be directly laminated on to human skin for reliable, sensitive bio-sensing but with minimal irritation to the user after long-time use. Excellent heat management films with strongly anisotropic thermal conductivity (K) and adequate breathability are increasingly desirable for shielding the skin from heating while allowing the skin to breathe properly. Here, interfacial self-assembly of a graphene oxide (GO) film covering an ambient-dried bacterial cellulose aerogel (AD-BCA) film followed by laser reduction was proposed to prepare laser-reduced GO (L-rGO)/AD-BCA bilayered films. The AD-BCA substrate provides low cross-plane K (K ⊥  ≈  0.052 W mK‑1), high breathability, and high compressive and tensile resistance by ‘partially’ inheriting the pore structure from bacterial cellulose (BC) gel. The introduction of an upper L-rGO film, which is only 0.31 wt% content, dramatically increases the in-plane K (K // ) from 0.3 W mK‑1 in AD-BCA to 10.72 W mK‑1 owing to the highly in-plane oriented, continuous, uniform assembling geometry of the GO film; while K ⊥ decreases to a lower value of 0.033 W mK‑1, mainly owing to the air pockets between L-rGO multilayers caused by the laser reduction. The bilayered films achieve a K // /K ⊥ of 325, which is substantially larger even than that of graphite and similar polymer composites. They permit high transmission rates for water vapor (416.78 g/m2/day, >204 g/m2/day of normal skin) and O2 (449.35 cm3/m2/day). The combination of strongly anisotropic thermal conductivity and adequate breathability facilitates applications in heat management in on-skin electronics.

Undernutrition among children under 5 years of age in Yemen: Role of adequate childcare provided by adults under conditions of food insecurity.

Science.gov (United States)

Al-Sobaihi, Saber; Nakamura, Keiko; Kizuki, Masashi

2016-01-01

Objective: This study examined the associations between the adequacy of childcare provided by adult caretakers and childhood undernutrition in rural Yemen, independent of household wealth and food consumption. Methods: We analyzed data of 3,549 children under the age of 5 years living in rural areas of Yemen based on the 2013 Yemen Baseline Survey of Mother and Child Health. Nutritional status was evaluated by the presence of underweight, stunting, and wasting according to the World Health Organization child growth standards. The impact of childcare including leaving children alone, putting older children into labor force, and the use of antenatal care while pregnant on child undernutrition was assessed and adjusted for food consumption by children, household composition, demographic and educational background of caretakers, and household wealth. Results: The prevalence of underweight, stunting, and wasting was 46.2%, 62.6%, and 11.1%, respectively. Not leaving children alone, keeping children out of the labor force, and use of antenatal care were associated with a lower risk of underweight (odds ratio [OR] = 0.84, P = 0.016; OR = 0.84, P = 0.036; and OR = 0.85, P = 0.042) and stunting (OR = 0.80, P = 0.004; OR = 0.82, P = 0.024; and OR = 0.78, P = 0.003). After further adjustment for food consumption, the associations between adequate childcare indicators and lower odds of stunting remained significant (OR = 0.73, P = 0.025; OR = 0.72, P = 0.046; and OR = 0.76, P = 0.038). Conclusions: A marked prevalence of stunting among rural children in Yemen was observed. Adequate childcare by adult caretakers in families is associated with a lower incidence of underweight and stunting among children under 5 years of age. Promoting adequate childcare by adult household members is a feasible option for reducing undernutrition among children in rural Yemen.

JS-K, a Nitric Oxide Prodrug, Has Enhanced Cytotoxicity in Colon Cancer Cells with Knockdown of Thioredoxin Reductase 1

Science.gov (United States)

Edes, Kornelia; Cassidy, Pamela; Shami, Paul J.; Moos, Philip J.

2010-01-01

Background The selenoenzyme thioredoxin reductase 1 has a complex role relating to cell growth. It is induced as a component of the cellular response to potentially mutagenic oxidants, but also appears to provide growth advantages to transformed cells by inhibiting apoptosis. In addition, selenocysteine-deficient or alkylated forms of thioredoxin reductase 1 have also demonstrated oxidative, pro-apoptotic activity. Therefore, a greater understanding of the role of thioredoxin reductase in redox initiated apoptotic processes is warranted. Methodology The role of thioredoxin reductase 1 in RKO cells was evaluated by attenuating endogenous thioredoxin reductase 1 expression with siRNA and then either inducing a selenium-deficient thioredoxin reductase or treatment with distinct redox challenges including, hydrogen peroxide, an oxidized lipid, 4-hydroxy-2-nonenol, and a nitric oxide donating prodrug. Thioredoxin redox status, cellular viability, and effector caspase activity were measured. Conclusions/Significance In cells with attenuated endogenous thioredoxin reductase 1, a stably integrated selenocysteine-deficient form of the enzyme was induced but did not alter either the thioredoxin redox status or the cellular growth kinetics. The oxidized lipid and the nitric oxide donor demonstrated enhanced cytotoxicity when thioredoxin reductase 1 was knocked-down; however, the effect was more pronounced with the nitric oxide prodrug. These results are consistent with the hypothesis that attenuation of the thioredoxin-system can promote apoptosis in a nitric oxide-dependent manner. PMID:20098717

Influence of dietary methionine on the metabolism of selenomethionine in rats

International Nuclear Information System (INIS)

Butler, J.A.; Beilstein, M.A.; Whanger, P.D.

1989-01-01

To determine the influence of methionine on selenomethionine (SeMet) metabolism, weanling male rats were fed for 8 wk a basal diet marginally deficient in sulfur amino acids, containing 2.0 micrograms selenium (Se)/g as DL-SeMet and supplemented with 0, 0.3, 0.6 or 1.2% DL-methionine. Increased dietary methionine caused decreased selenium deposition in all tissues examined but increased glutathione peroxidase activity in testes, liver and lungs. A positive correlation was found between dietary methionine and the calculated percentage of selenium associated with GSHPx. In a second experiment, 75 SeMet was injected into weanling male rats which had been fed the basal diet containing 2.0 micrograms selenium as DL-SeMet with or without the addition of 1.0% methionine. The selenoamino acid content of tissues and the distribution of 75 Se in erythrocyte proteins were determined. In comparison to the rats fed the basal diet without added methionine, significantly more 75 Se-selenocysteine was found in liver and muscle, more 75 Se was found in erythrocyte GSHPx and less 75 Se was found in erythrocyte hemoglobin of rats fed 1.0% methionine. These data suggest that methionine diverts SeMet from incorporation into general proteins and enhances its conversion to selenocysteine for specific selenium-requiring proteins, such as GSHPx

GENERIC APPROACH IN CHOICE OF ADEQUATE METHODOLOGY FOR THE ASSESSMENT OF IT INVESTMENTS

Directory of Open Access Journals (Sweden)

Melita Kozina

2012-07-01

Full Text Available Investments into information technology (IT, (hereinafter: IT investments havereached very high figures, which are still continually on the rise. IT potentials are being usedin an increasing number of ways. Various company managers have different approaches tothis issue. A large number of methods/models for the assessment of IT investments isavailable, so the question is posed of how to choose the adequate assessment category. Thesaid reasons have initiated a need for defining the generic approach in the choice ofadequate methodology for the assessment of IT investments, which was indeed the goal ofthis paper. General ideas to this approach stem from the fact that each IT investment has itspurpose and belongs to a certain type of IT investment (decision-making aspect whichdemands its relevant methodology for assessing IT investments. Two groups of demands(conditions have been defined in choosing relevant methodology. The first group pertains tomethodology analysis and determination of its compatibility with characteristics of thedefined decision-making aspect. The second group of conditions pertains to methodologyanalysis with respect to its possibilities (abilities of integrating quantity, quality and riskfactors of IT decision. Conducted field research shows that the assessment of IT investmentshas been done mainly using simpler methods/models and their combinations, and is focusedon quantity aspects of IT values.

The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.

Science.gov (United States)

Rodnina, Marina V; Wintermeyer, Wolfgang

2011-04-01

Translocation of tRNA and mRNA through the ribosome is one of the most dynamic events during protein synthesis. In the cell, translocation is catalysed by EF-G (elongation factor G) and driven by GTP hydrolysis. Major unresolved questions are: how the movement is induced and what the moving parts of the ribosome are. Recent progress in time-resolved cryoelectron microscopy revealed trajectories of tRNA movement through the ribosome. Driven by thermal fluctuations, the ribosome spontaneously samples a large number of conformational states. The spontaneous movement of tRNAs through the ribosome is loosely coupled to the motions within the ribosome. EF-G stabilizes conformational states prone to translocation and promotes a conformational rearrangement of the ribosome (unlocking) that accelerates the rate-limiting step of translocation: the movement of the tRNA anticodons on the small ribosomal subunit. EF-G acts as a Brownian ratchet providing directional bias for movement at the cost of GTP hydrolysis.

Hidden layers of human small RNAs

DEFF Research Database (Denmark)

Kawaji, Hideya; Nakamura, Mari; Takahashi, Yukari

2008-01-01

small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs. RESULTS: Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19-40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data......BACKGROUND: Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile...... shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both...

Interactions ARN-protéines dans le mécanisme de biosynthèse des sélénoprotéines

OpenAIRE

Takeuchi , Akiko

2009-01-01

The 21st amino acid selenocysteine is encoded by a UGA codon that usually signifies translational termination. Selenoprotein synthesis therefore requires specialized factors. Among these is SBP2 that binds the SECIS, a stem-loop structure in the 3'UTR of selenoprotein mRNAs. In structural analyses of SBP2, we isolated and functionally characterized Drosophila melanogaster SBP2. By comparing it with human SBP2, we identified an additional RNA binding domain that is essential for SECIS and 60S ...

The Comprehension Problems of Children with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

Science.gov (United States)

Spencer, Mercedes; Wagner, Richard K

2018-06-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language (vocabulary, listening comprehension, storytelling ability, and semantic and syntactic knowledge). Results indicated that children with SCD had deficits in oral language ( d = -0.78, 95% CI [-0.89, -0.68], but these deficits were not as severe as their deficit in reading comprehension ( d = -2.78, 95% CI [-3.01, -2.54]). When compared to reading comprehension age-matched normal readers, the oral language skills of the two groups were comparable ( d = 0.32, 95% CI [-0.49, 1.14]), which suggests that the oral language weaknesses of children with SCD represent a developmental delay rather than developmental deviance. Theoretical and practical implications of these findings are discussed.

Enzymatic synthesis of tRNA-peptide conjugates and spectroscopic studies of fluorine-modified RNA

International Nuclear Information System (INIS)

Graber, D.

2010-01-01

The research presented in this thesis concerns the enzymatic synthesis of artificially modified tRNA, in particular the preparation of non-hydrolysable tRNA-peptide conjugates. Another focus is on NMR-spectroscopic investigations of fluorine-modified RNA. In both projects, chemical methods were developed to address specific RNA-biological research questions. In the first part of this thesis the preparation of tRNA-peptide conjugates with a non-hydrolysable 3'-amide linkage is presented. These molecules are of high relevance for the characterization of ribosomal processes that occur in the peptidyl transferase center (such as peptide bond formation, peptide release, or translocation) using X-ray crystallography and biochemical methods. First, a novel concept to prepare chemically modified ('labeled') tRNA was elaborated based on the combination of solid-phase synthesis and enzymatic ligation. Thereby, a variety of differently labeled tRNAs was achieved. Moreover, the most successful high-yield ligation sites were identified to be situated within the TΨ C-loop. Optimization of the synthesis and the corresponding HPLC-purification of the conjugates were initially conducted with puromycin derivatized tRNA. In the course of this project, also two tRNAs with a ribose 3'-amino group at the terminal adenosine A76 were synthesized. For that purpose a protection group pattern had to be developed to obtain a functionalized solid-support bound to 3'-amino-3'-deoxyadenosine which was appropriate for RNA solid-phase synthesis. The successful preparation of tRNA-peptide conjugates was accomplished in cooperation with Holger Moroder and Jessica Steger (Micura group) who contributed short synthetic RNA-peptide conjugates. These fragments represented the tRNA 3'-termini that were required for exploring the new ligation strategies for non-hydrolisable tRNA - a main aim of this thesis. If the 5'-fragments are synthesized by solid-phase synthesis or in vitro transcription they do not

Impact of Rabies Vaccination History on Attainment of an Adequate Antibody Titre Among Dogs Tested for International Travel Certification, Israel - 2010-2014.

Science.gov (United States)

Yakobson, B; Taylor, N; Dveres, N; Rotblat, S; Spero, Ż; Lankau, E W; Maki, J

2017-06-01

Rabies is endemic in wildlife or domestic carnivore populations globally. Infection of domestic dogs is of particular concern in many areas. In regions where domestic animals are at risk of exposure to rabies virus, dogs should be routinely vaccinated against rabies to protect both pet and human populations. Many countries require demonstration of an adequate level of serum rabies neutralizing antibodies to permit entry of dogs during international travel. We analysed rabies titres of dogs seeking travel certification in Israel to assess demographic and vaccine history factors associated with antibody titres below the acceptable threshold for travel certification. Having received only one previous rabies vaccination and a longer duration since the most recent vaccination was received were primary risk factors for not achieving an adequate rabies virus neutralizing antibody titre for travel certification. These risk factors had stronger effects in younger animals, but were consistent for dogs of all ages. In particular, these findings reiterate the importance of administering at least two rabies vaccinations (the primo vaccination and subsequent booster) to ensure population-level protection against rabies in dogs globally. © 2016 Blackwell Verlag GmbH.

Exploiting tRNAs to Boost Virulence

Directory of Open Access Journals (Sweden)

Suki Albers

2016-01-01

Full Text Available Transfer RNAs (tRNAs are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it difficult to characterize individual species quantitatively. However, due to the central role of the tRNA pool in protein biosynthesis as well as newly emerging roles played by tRNAs, their quantitative assessment yields important information, particularly relevant for virus research. Viruses which depend on the host protein expression machinery have evolved various strategies to optimize tRNA usage—either by adapting to the host codon usage or encoding their own tRNAs. Additionally, several viruses bear tRNA-like elements (TLE in the 5′- and 3′-UTR of their mRNAs. There are different hypotheses concerning the manner in which such structures boost viral protein expression. Furthermore, retroviruses use special tRNAs for packaging and initiating reverse transcription of their genetic material. Since there is a strong specificity of different viruses towards certain tRNAs, different strategies for recruitment are employed. Interestingly, modifications on tRNAs strongly impact their functionality in viruses. Here, we review those intersection points between virus and tRNA research and describe methods for assessing the tRNA pool in terms of concentration, aminoacylation and modification.

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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Adequate nutrition status important for bone mineral density improvement in a patient with anorexia nervosa

Directory of Open Access Journals (Sweden)

Nakamura Y

2018-05-01

Full Text Available Yukio Nakamura,1,2 Mikio Kamimura,3 Hidefumi Koiwai,4 Hiroyuki Kato1 1Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan; 2Department of Orthopedic Surgery, Showa-Inan General Hospital, Komagane, Japan; 3Center of Osteoporosis and Spinal Disorders, Kamimura Orthopedic Clinic, Matsumoto, Japan; 4Koiwai Orthopedic Clinic, Komoro, Japan Abstract: Low bone mineral density (BMD is one of the most frequent complications of anorexia nervosa (AN. We report the clinical outcomes of a female patient with severe AN, whose chest had become deformed due to thoracic fracture. Lumbar BMD was 0.358 g/cm2 (T-score = −6.3, and total hip BMD was 0.411 g/cm2 (T-score = −4.4. Active vitamin D increased these parameters by 81.0% and 57.4%, respectively, but a drop in her nutrition status afterward resulted in a sharp decrease in BMD values. These findings suggest that adequate nutrient intake is essential for effective osteoporosis treatment in patients with AN. Keywords: anorexia nervosa, bone mineral density, daily teriparatide, osteoporosis

Structural studies of a bacterial tRNA(HIS guanylyltransferase (Thg1-like protein, with nucleotide in the activation and nucleotidyl transfer sites.

Directory of Open Access Journals (Sweden)

Samantha J Hyde

Full Text Available All nucleotide polymerases and transferases catalyze nucleotide addition in a 5' to 3' direction. In contrast, tRNA(His guanylyltransferase (Thg1 enzymes catalyze the unusual reverse addition (3' to 5' of nucleotides to polynucleotide substrates. In eukaryotes, Thg1 enzymes use the 3'-5' addition activity to add G-1 to the 5'-end of tRNA(His, a modification required for efficient aminoacylation of the tRNA by the histidyl-tRNA synthetase. Thg1-like proteins (TLPs are found in Archaea, Bacteria, and mitochondria and are biochemically distinct from their eukaryotic Thg1 counterparts TLPs catalyze 5'-end repair of truncated tRNAs and act on a broad range of tRNA substrates instead of exhibiting strict specificity for tRNA(His. Taken together, these data suggest that TLPs function in distinct biological pathways from the tRNA(His maturation pathway, perhaps in tRNA quality control. Here we present the first crystal structure of a TLP, from the gram-positive soil bacterium Bacillus thuringiensis (BtTLP. The enzyme is a tetramer like human THG1, with which it shares substantial structural similarity. Catalysis of the 3'-5' reaction with 5'-monophosphorylated tRNA necessitates first an activation step, generating a 5'-adenylylated intermediate prior to a second nucleotidyl transfer step, in which a nucleotide is transferred to the tRNA 5'-end. Consistent with earlier characterization of human THG1, we observed distinct binding sites for the nucleotides involved in these two steps of activation and nucleotidyl transfer. A BtTLP complex with GTP reveals new interactions with the GTP nucleotide in the activation site that were not evident from the previously solved structure. Moreover, the BtTLP-ATP structure allows direct observation of ATP in the activation site for the first time. The BtTLP structural data, combined with kinetic analysis of selected variants, provide new insight into the role of key residues in the activation step.

Hili Inhibits HIV Replication in Activated T Cells.

Science.gov (United States)

Peterlin, B Matija; Liu, Pingyang; Wang, Xiaoyun; Cary, Daniele; Shao, Wei; Leoz, Marie; Hong, Tian; Pan, Tao; Fujinaga, Koh

2017-06-01

P-element-induced wimpy-like (Piwil) proteins restrict the replication of mobile genetic elements in the germ line. They are also expressed in many transformed cell lines. In this study, we discovered that the human Piwil 2 (Hili) protein can also inhibit HIV replication, especially in activated CD4 + T cells that are the preferred target cells for this virus in the infected host. Although resting cells did not express Hili, its expression was rapidly induced following T cell activation. In these cells and transformed cell lines, depletion of Hili increased levels of viral proteins and new viral particles. Further studies revealed that Hili binds to tRNA. Some of the tRNAs represent rare tRNA species, whose codons are overrepresented in the viral genome. Targeting tRNA Arg (UCU) with an antisense oligonucleotide replicated effects of Hili and also inhibited HIV replication. Finally, Hili also inhibited the retrotransposition of the endogenous intracysternal A particle (IAP) by a similar mechanism. Thus, Hili joins a list of host proteins that inhibit the replication of HIV and other mobile genetic elements. IMPORTANCE Piwil proteins inhibit the movement of mobile genetic elements in the germ line. In their absence, sperm does not form and male mice are sterile. This inhibition is thought to occur via small Piwi-interacting RNAs (piRNAs). However, in some species and in human somatic cells, Piwil proteins bind primarily to tRNA. In this report, we demonstrate that human Piwil proteins, especially Hili, not only bind to select tRNA species, including rare tRNAs, but also inhibit HIV replication. Importantly, T cell activation induces the expression of Hili in CD4 + T cells. Since Hili also inhibited the movement of an endogenous retrovirus (IAP), our finding shed new light on this intracellular resistance to exogenous and endogenous retroviruses as well as other mobile genetic elements. Copyright © 2017 American Society for Microbiology.

Effects of the antituberculous drug ethambutol on zinc absorption, turnover and distribution in rats fed diet marginal and adequate in zinc

Energy Technology Data Exchange (ETDEWEB)

King, A.B.; Schwartz, R.

1987-04-01

Ethambutol, (CH/sub 3/CH/sub 2/-CH(CH/sub 2/OH)-NH-CH/sub 2/)/sub 2/ (EMB), is an oral antituberculous agent that is administered therapeutically over extended time periods. It has chelating properties and may affect mineral metabolism. Male weanling Sprague-Dawley rats received 0, 400 or 600 mg EMB per kilogram body weight daily by gavage for 30 d. They were fed a casein-based diet with either adequate (49 ppm) or marginal (11 ppm) zinc. Both adequate-Zn (AZn) and marginal-Zn (MZn) rats receiving EMB showed alopecia and dose-dependent reductions in feed intake, weight gain and feed efficiency. None of these changes was seen in rats fed the MZn diet without EMB. Serum and tissue zinc levels were similar in rats not receiving EMB, regardless of the dietary zinc level. Serum zinc was consistently lower in AZn and MZn rats receiving EMB than in rats without EMB. Apparent zinc absorption, measured by /sup 65/Zn balance, was higher in AZn rats receiving EMB than in AZn rats without EMB. Thus, changes in absorption could not account for lower serum zinc levels in EMB-treated rats. However, /sup 65/Zn turnover was also higher in EMB groups. This suggests that EMB may have increased urinary zinc losses resulting in reduced circulating zinc and a consequent increase in zinc absorption.

Effects of the antituberculous drug ethambutol on zinc absorption, turnover and distribution in rats fed diet marginal and adequate in zinc

International Nuclear Information System (INIS)

King, A.B.; Schwartz, R.

1987-01-01

Ethambutol, [CH 3 CH 2 -CH(CH 2 OH)-NH-CH 2 ] 2 (EMB), is an oral antituberculous agent that is administered therapeutically over extended time periods. It has chelating properties and may affect mineral metabolism. Male weanling Sprague-Dawley rats received 0, 400 or 600 mg EMB per kilogram body weight daily by gavage for 30 d. They were fed a casein-based diet with either adequate (49 ppm) or marginal (11 ppm) zinc. Both adequate-Zn (AZn) and marginal-Zn (MZn) rats receiving EMB showed alopecia and dose-dependent reductions in feed intake, weight gain and feed efficiency. None of these changes was seen in rats fed the MZn diet without EMB. Serum and tissue zinc levels were similar in rats not receiving EMB, regardless of the dietary zinc level. Serum zinc was consistently lower in AZn and MZn rats receiving EMB than in rats without EMB. Apparent zinc absorption, measured by 65 Zn balance, was higher in AZn rats receiving EMB than in AZn rats without EMB. Thus, changes in absorption could not account for lower serum zinc levels in EMB-treated rats. However, 65 Zn turnover was also higher in EMB groups. This suggests that EMB may have increased urinary zinc losses resulting in reduced circulating zinc and a consequent increase in zinc absorption

Development of adequate meteorological monitoring standards for safety analysis of nuclear facilities

International Nuclear Information System (INIS)

Alp, E.; Lewis, P.J.

1985-09-01

The aim of this report is to identify what constitutes adequate meteorological information for airborne dispersion calculations in case of releases from nuclear facilities during 'normal operation', 'design postulated accidents', and 'emergency situations'. The models used for estimating downwind dispersion are reviewed, including short-range simple terrain, short-range complex terrain and medium to long range models with emphasis on Lagrangian models. The meteorogolical input parameters required for running these models are identified. The methods by which these parameters may be obtained from raw meteorological data are then considered. Emphasis is placed on well-tried and recommended methods rather than those which are currently being developed and lack long-term field tests. The meteorological data required to calculate the parameters that are in turn input to dispersion calculation methods can be obtained mainly from tower measurements. Recommended tower height is 50 m, with two levels of instruments (10 and 50 m) for wind speed, wind direction and temperature. Data for precipitation and solar radiation, that may be required under certain conditions and for special calculations, may be estimated from nearby representative weather stations (if available). For simple terrain, a single tower is sufficient. For complex terrain, such as coastal regions, two towers are desirable for accurate characterization of the turbulence regime in the vicinity of a release site. The report provides the necessary accuracy specifications for instruments required for the meteorological measurements. Data monitoring and recording, maintenance, quality control and assurance are also discussed. Error propagation analyses are recommended to determine the full implications of instrument accuracies on the accuracy of dispersion model predictions. 82 refs

Maintaining Adequate Carbon Dioxide Washout for an Advanced Extravehicular Mobility Unit

Science.gov (United States)

Chullen, Cinda; Navarro, Moses; Conger, Bruce; Korona, Adam; McMillin, Summer; Norcross, Jason; Swickrath, Mike

2013-01-01

Over the past several years, NASA has realized tremendous progress in technology development that is aimed at the production of an Advanced Extravehicular Mobility Unit (AEMU). Of the many functions provided by the spacesuit and portable life support subsystem within the AEMU, delivering breathing gas to the astronaut along with removing the carbon dioxide (CO2) remains one of the most important environmental functions that the AEMU can control. Carbon dioxide washout is the capability of the ventilation flow in the spacesuit helmet to provide low concentrations of CO2 to the crew member to meet breathing requirements. CO2 washout performance is a critical parameter needed to ensure proper and sufficient designs in a spacesuit and in vehicle applications such as sleep stations and hygiene compartments. Human testing to fully evaluate and validate CO2 washout performance is necessary but also expensive due to the levied safety requirements. Moreover, correlation of math models becomes challenging because of human variability and movement. To supplement human CO2 washout testing, a breathing capability will be integrated into a suited manikin test apparatus to provide a safe, lower cost, stable, easily modeled alternative to human testing. Additionally, this configuration provides NASA Johnson Space Center (JSC) the capability to evaluate CO2 washout under off-nominal conditions that would otherwise be unsafe for human testing or difficult due to fatigue of a test subject. Testing has been under way in-house at JSC and analysis has been initiated to evaluate whether the technology provides sufficient 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 extravehicular activity. This paper will review recent CO2 washout testing and analysis activities, testing planned in-house with a spacesuit simulator, and the associated analytical work

First adequately-known quadrupedal sirenian from Eurasia (Eocene, Bay of Biscay, Huesca, northeastern Spain).

Science.gov (United States)

Díaz-Berenguer, Ester; Badiola, Ainara; Moreno-Azanza, Miguel; Canudo, José Ignacio

2018-03-23

Sirenians are the only extant herbivorous mammals fully adapted to an aquatic lifestyle. They originated in Africa during the Paleocene from an undetermined clade of afrotherian mammals, and by the end of the Eocene they were widely distributed across the tropical latitudes. Here we introduce Sobrarbesiren cardieli gen. et sp. nov. It is the first adequately-known quadrupedal sirenian from Eurasia and the oldest record of this clade from western Europe. Fossils have been recovered from the middle Lutetian (SBZ15) site of Castejón de Sobrarbe-41 (Huesca, Spain), and comprise many cranial and postcranial remains, including pelvic girdle and hind limb bones, from at least six sirenian individuals of different ontogenetic stages. Sobrarbesiren shows a suite of characters previously considered synapomorphies of different clades of derived sirenians, such as the presence of the processus retroversus of the squamosal and the pterygoid fossa, combined with ancestral characters such as the presence of an alisphenoid canal, a permanent P5, at least two sacral vertebrae, a primitive pelvis and functional femora and fibulae. Sobrarbesiren is recovered as the sister taxon of Dugongidae and represents a transitional stage of adaptation to aquatic life between the amphibious quadrupedal prorastomids and the aquatic quadrupedal protosirenids.

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.

Proposal for a advanced PWR core with adequate characteristics for passive safety concept

International Nuclear Information System (INIS)

Perrotta, Jose Augusto

1999-01-01

This work presents a discussion upon the suitable from an advanced PWR core, classified by the EPRI as 'Passive PWR' (advanced reactor with passive safety concept to power plants with less than 600 MW electrical power). The discussion upon the type of core is based on nuclear fuel engineering concepts. Discussion is made on type of fuel materials, structural materials, geometric shapes and manufacturing process that are suitable to produce fuel assemblies which give good performance for this type of reactors. The analysis is guided by the EPRI requirements for Advanced Light Water Reactor (ALWR). By means of comparison, the analysis were done to Angra 1 (old type of 600 MWe PWR class), and the design of the Westinghouse Advanced PWR-AP600. It was verified as a conclusion of this work that the modern PWR fuels are suitable for advanced PWR's Nevertheless, this work presents a technical alternative to this kind of fuel, still using UO 2 as fuel, but changing its cylindrical form of pellets and pin type fuel element to plane shape pallets and plate type fuel element. This is not a novelty fuel, since it was used in the 50's at Shippingport Reactor and as an advanced version by CEA of France in the 70's. In this work it is proposed a new mechanical assembly design for this fuel, which can give adequate safety and operational performance to the core of a 'Passive PWR'. (author)

Complete mitochondrial genome of the mottled skate: Raja pulchra (Rajiformes, Rajidae).

Science.gov (United States)

Jeong, Dageum; Kim, Sung; Kim, Choong-Gon; Myoung, Jung-Goo; Lee, Youn-Ho

2016-05-01

The complete sequence of mitochondrial DNA of a mottled skate, Raja pulchra was sequenced as being circular molecules of 16,907 bp including 2 rRNA, 22 tRNA, 13 protein-coding genes (PCGs), and an AT-rich control region. The organization of the PCGs is the same as those found in other Rajidae species. The nucleotide of L-strand is composed of 29.8% A, 28.0% C, 27.9% T, and 14.3% G with a bias toward A + T slightly. Twelve of 13 PCGs are initiated by the ATG codon while COX1 starts with GTG. Only ND4 harbors the incomplete termination codon, TA. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA with the exception of [Formula: see text] which has a reduced DHU arm. This mitogenome will provide essential information for better phylogenetic resolution and precision of the family Rajidae and the genus Raja as well as for establishment of a fish stock recovery plan of the species.

Complete mitochondrial genome of the Kwangtung skate: Dipturus kwangtungensis (Rajiformes, Rajidae).

Science.gov (United States)

Jeong, Dageum; Kim, Sung; Kim, Choong-Gon; Lee, Youn-Ho

2015-01-01

The complete sequence of mitochondrial DNA of a Kwangtung skate, Dipturus kwangtungensis, was determined as being circular molecules of 16,912 bp including 2 rRNA, 22 tRNA, 13 protein coding genes (PCGs) and a control region. The arrangement of the PCGs is the same as that found in other Rajidae species. The nucleotide of L-strand which encodes most of the proteins is composed of 30.2% A, 27.4% C, 28.2% T and 14.2% G with a bias toward A+T slightly. Twelve of 13 PCGs are initiated by the ATG codon while COX1 starts with GTG. Only ND4 harbors the incomplete termination codon, TA. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA with the exception of tRNA(Ser)AGY, which has a reduced DHU arm. This mitogenome is the first report for a species of the genus Dipturus, which will become an important source of information on the phylogenetic relationship and the evolution of the genus Dipturus within the family Rajidae.

The flavoprotein Mcap0476 (RlmFO) catalyzes m5U1939 modification in Mycoplasma capricolum 23S rRNA

DEFF Research Database (Denmark)

Lartigue, Carole; Lebaudy, Anne; Blanchard, Alain

2014-01-01

Efficient protein synthesis in all organisms requires the post-transcriptional methylation of specific ribosomal ribonucleic acid (rRNA) and transfer RNA (tRNA) nucleotides. The methylation reactions are almost invariably catalyzed by enzymes that use S-adenosylmethionine (AdoMet) as the methyl g...... specifically modifies m5U1939 in 23S rRNA, a conserved methylation catalyzed by AdoMet-dependent enzymes in all other characterized bacteria. The Mcap0476 methyltransferase (renamed RlmFO) represents the first folate-dependent flavoprotein seen to modify ribosomal RNA.......Efficient protein synthesis in all organisms requires the post-transcriptional methylation of specific ribosomal ribonucleic acid (rRNA) and transfer RNA (tRNA) nucleotides. The methylation reactions are almost invariably catalyzed by enzymes that use S-adenosylmethionine (AdoMet) as the methyl...... group donor. One noteworthy exception is seen in some bacteria, where the conserved tRNA methylation at m5U54 is added by the enzyme TrmFO using flavin adenine dinucleotide together with N5,N10-methylenetetrahydrofolate as the one-carbon donor. The minimalist bacterium Mycoplasma capricolum possesses...

Decoding options and accuracy of translation of developmentally regulated UUA codon in Streptomyces: bioinformatic analysis.

Science.gov (United States)

Rokytskyy, Ihor; Koshla, Oksana; Fedorenko, Victor; Ostash, Bohdan

2016-01-01

The gene bldA for leucyl [Formula: see text] is known for almost 30 years as a key regulator of morphogenesis and secondary metabolism in genus Streptomyces. Codon UUA is the rarest one in Streptomyces genomes and is present exclusively in genes with auxiliary functions. Delayed accumulation of translation-competent [Formula: see text] is believed to confine the expression of UUA-containing transcripts to stationary phase. Implicit to the regulatory function of UUA codon is the assumption about high accuracy of its translation, e.g. the latter should not occur in the absence of cognate [Formula: see text]. However, a growing body of facts points to the possibility of mistranslation of UUA-containing transcripts in the bldA-deficient mutants. It is not known what type of near-cognate tRNA(s) may decode UUA in the absence of cognate tRNA in Streptomyces, and whether UUA possesses certain inherent properties (such as increased/decreased accuracy of decoding) that would favor its use for regulatory purposes. Here we took bioinformatic approach to address these questions. We catalogued the entire complement of tRNA genes from several relevant Streptomyces and identified genes for posttranscriptional modifications of tRNA that might be involved in UUA decoding by cognate and near-cognate tRNAs. Based on tRNA gene content in Streptomyces genomes, we propose possible scenarios of UUA codon mistranslation. UUA is not associated with an increased rate of missense errors as compared to other leucyl codons, contrasting general belief that low-abundant codons are more error-prone than the high-abundant ones.

Children with Disabilities Are Often Misdiagnosed Initially and Children with Neuropsychiatric Disorders Are Referred to Adequate Resources 30 Months Later than Children with Other Disabilities

Science.gov (United States)

Tuominen-Eriksson, Alli-Marie; Svensson, Yvonne; Gunnarsson, Ronny K.

2013-01-01

Disabilities in a child may lead to low self-esteem and social problems. The lives of parents and siblings are also affected. Early intervention may decrease these consequences. To promote early intervention early referral to adequate resources is essential. In a longitudinal retrospective observational study it was found that children with…

Do Foley Catheters Adequately Drain the Bladder? Evidence from CT Imaging Studies

Directory of Open Access Journals (Sweden)

Svetlana Avulova

2015-06-01

Full Text Available ABSTRACTIntroduction: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 tomo-graphic (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

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)

The OECD agreement on exchange of information on tax matters : an analysis of its adequateness as a tool to combat tax havens

OpenAIRE

Fossland, Tine

2011-01-01

The aim with this thesis is to investigate whether Tax Information Exchange Agreements (TIEA) serve as adequate tools to combat the existence of tax havens and its harmful consequences. More specifically, this thesis pursues to establish what features of tax havens that the OECD Agreement on Exchange of Information on Tax Matters helps putting a stop to, and what characteristics of a tax haven that the respective agreement is unable to stop. The thesis is organized as follows. ...

Analysis of clinical data to determine the minimum number of sensors required for adequate skin temperature monitoring of superficial hyperthermia treatments.

Science.gov (United States)

Bakker, Akke; Holman, Rebecca; Rodrigues, Dario B; Dobšíček Trefná, Hana; Stauffer, Paul R; van Tienhoven, Geertjan; Rasch, Coen R N; Crezee, Hans

2018-04-27

Tumor response and treatment toxicity are related to minimum and maximum tissue temperatures during hyperthermia, respectively. Using a large set of clinical data, we analyzed the number of sensors required to adequately monitor skin temperature during superficial hyperthermia treatment of breast cancer patients. Hyperthermia treatments monitored with >60 stationary temperature sensors were selected from a database of patients with recurrent breast cancer treated with re-irradiation (23 × 2 Gy) and hyperthermia using single 434 MHz applicators (effective field size 351-396 cm 2 ). Reduced temperature monitoring schemes involved randomly selected subsets of stationary skin sensors, and another subset simulating continuous thermal mapping of the skin. Temperature differences (ΔT) between subsets and complete sets of sensors were evaluated in terms of overall minimum (T min ) and maximum (T max ) temperature, as well as T90 and T10. Eighty patients were included yielding a total of 400 hyperthermia sessions. Median ΔT was 50 sensors were used. Subsets of sensors result in underestimation of T max up to -2.1 °C (ΔT 95%CI), which decreased to -0.5 °C when >50 sensors were used. Thermal profiles (8-21 probes) yielded a median ΔT 50 stationary sensors or thermal profiles. Adequate coverage of the skin temperature distribution during superficial hyperthermia treatment requires the use of >50 stationary sensors per 400 cm 2 applicator. Thermal mapping is a valid alternative.

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate

DEFF Research Database (Denmark)

Wang, Xuzhen; Wang, Jun; He, Shunping

2007-01-01

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes, and a no......The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes...

Enhancement of single-molecule fluorescence signals by colloidal silver nanoparticles in studies of protein translation.

Science.gov (United States)

Bharill, Shashank; Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskiran; Smilansky, Zeev; Mandecki, Wlodek; Gryczynski, Ignacy; Gryczynski, Zygmunt; Cooperman, Barry S; Goldman, Yale E

2011-01-25

Metal-enhanced fluorescence (MEF) increased total photon emission of Cy3- and Cy5-labeled ribosomal initiation complexes near 50 nm silver particles 4- and 5.5-fold, respectively. Fluorescence intensity fluctuations above shot noise, at 0.1-5 Hz, were greater on silver particles. Overall signal-to-noise ratio was similar or slightly improved near the particles. Proximity to silver particles did not compromise ribosome function, as measured by codon-dependent binding of fluorescent tRNA, dynamics of fluorescence resonance energy transfer between adjacent tRNAs in the ribosome, and tRNA translocation induced by elongation factor G.

Enhancement of Single Molecule Fluorescence Signals by Colloidal Silver Nanoparticles in Studies of Protein Translation

Science.gov (United States)

Bharill, Shashank; Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskiran; Smilansky, Zeev; Mandecki, Wlodek; Gryczynski, Ignacy; Gryczynski, Zygmunt; Cooperman, Barry S.; Goldman, Yale E.

2011-01-01

Metal enhanced fluorescence (MEF) increased total photon emission of Cy3- and Cy5-labeled ribosomal initiation complexes near 50 nm silver particles 4- and 5.5-fold respectively. Fluorescence intensity fluctuations above shot noise, at 0.1 – 5 Hz, were greater on silver particles. Overall signal to noise ratio was similar or slightly improved near the particles. Proximity to silver particles did not compromise ribosome function, as measured by codon-dependent binding of fluorescent tRNA, dynamics of fluorescence resonance energy transfer between adjacent tRNAs in the ribosome, and tRNA translocation induced by elongation factor G. PMID:21158483

The Goal of Adequate Nutrition: Can It Be Made Affordable, Sustainable, and Universal?

Directory of Open Access Journals (Sweden)

Ian McFarlane

2016-11-01

Full Text Available Until about 1900, large proportions of the world population endured hunger and poverty. The 20th century saw world population increase from 1.6 to 6.1 billion, accompanied and to some extent made possible by rapid improvements in health standards and food supply, with associated advances in agricultural and nutrition sciences. In this paper, I use the application of linear programming (LP in preparation of rations for farm animals to illustrate a method of calculating the lowest cost of a human diet selected from locally available food items, constrained to provide recommended levels of food energy and nutrients; then, to find a realistic minimum cost, I apply the further constraint that the main sources of food energy in the costed diet are weighted in proportion to the actual reported consumption of food items in that area. Worldwide variations in dietary preferences raise the issue as to the sustainability of popular dietary regimes, and the paper reviews the factors associated with satisfying requirements for adequate nutrition within those regimes. The ultimate physical constraints on food supply are described, together with the ways in which climate change may affect those constraints. During the 20th century, food supply increased sufficiently in most areas to keep pace with the rapid increase in world population. Many challenges will need to be overcome if food supply is to continue to meet demand, and those challenges are made more severe by rising expectations of quality of life in the developing world, as well as by the impacts of climate change on agriculture and aquaculture.

Prediction of Adequate Prenatal Care Utilization Based on the Extended Parallel Process Model.

Science.gov (United States)

Hajian, Sepideh; Imani, Fatemeh; Riazi, Hedyeh; Salmani, Fatemeh

2017-10-01

Pregnancy complications are one of the major public health concerns. One of the main causes of preventable complications is the absence of or inadequate provision of prenatal care. The present study was conducted to investigate whether Extended Parallel Process Model's constructs can predict the utilization of prenatal care services. The present longitudinal prospective study was conducted on 192 pregnant women selected through the multi-stage sampling of health facilities in Qeshm, Hormozgan province, from April to June 2015. Participants were followed up from the first half of pregnancy until their childbirth to assess adequate or inadequate/non-utilization of prenatal care services. Data were collected using the structured Risk Behavior Diagnosis Scale. The analysis of the data was carried out in SPSS-22 using one-way ANOVA, linear regression and logistic regression analysis. The level of significance was set at 0.05. Totally, 178 pregnant women with a mean age of 25.31±5.42 completed the study. Perceived self-efficacy (OR=25.23; Pprenatal care. Husband's occupation in the labor market (OR=0.43; P=0.02), unwanted pregnancy (OR=0.352; Pcare for the minors or elderly at home (OR=0.35; P=0.045) were associated with lower odds of receiving prenatal care. The model showed that when perceived efficacy of the prenatal care services overcame the perceived threat, the likelihood of prenatal care usage will increase. This study identified some modifiable factors associated with prenatal care usage by women, providing key targets for appropriate clinical interventions.

Multiple giant succular and fusiform right and left coronary artery aneurysms after early and adequate treatment of atypical kawasaki disease with unusual presentation.

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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.

Poor neurological sequelae of herpes simplex virus encephalitis in an infant despite adequate antiviral and adjunct corticosteroid therapy

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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.

Effect of intramolecular photochemical cross-linking and of alkylation of 4-thiouridine in E. coli tRNAsub(l)sup(Val). On the heterologous misccharging by yeast phenylalanyl-tRNA synthetase

Energy Technology Data Exchange (ETDEWEB)

Kumar, S A; Krauskopf, M; Ofengand, J [Roche Inst. of Molecular Biology, Nutley, N.J. (USA)

1973-08-01

The ability of yeast phenylalanyl-tRNA synthetase to carry out the heterologous mischarging of nine E. coli tRNAs with phenylalanine, and the presence of a common sequence in these tRNAs in the double stranded region adjacent to the dihydrouridine loop, have led to the proposal (by Dudock) that this region of the tRNA is involved in recognition by the yeast enzyme. The validity of this hypothesis has now been examined by chemical modification of the region in question using as a test tRNA, E. coli tRNA/sub 1/sup( val). Photochemical cross-linking of /sup 4/S(8) and C(13) by irradiation at 335 nm led to a complete loss of the ability of yeast phenylalanyl-tRNA synthetase to functionally recognize tRNA/sub 1/sup( val) and the rate of cross-linking was correlated with the rate of loss of activity when appropriate assay conditions were used. Cross-linking had no effect on the recognition by the homologous E. coli valyl-tRNA synthetase (EC 6.1.1.9). Similarly, S-alkylation of the /sup 4/S(8) residue with iodoacetamide at pH 9 yielded the uridine-4-thio(2-acetamide) derivative of tRNA with no loss of homologous recognition but with complete loss of heterologous charging activity. These results provide evidence that at least part of the yeast phenylalanyl-tRNA synthetase recognition site is located in the region of the tRNA proposed by Dudock, and, as a corollary, show that the E. coli valyl-tRNA synthetase recognition site(s) must be elsewhere in the molecule.

Parieto-occipital hypoaccumulation of {sup 123}I-IMP in the brain SPECT associated with maternal inheritance of diabetes mellitus

Energy Technology Data Exchange (ETDEWEB)

Suzuki, Yoshihiko; Atsumi, Yoshihito; Hosokawa, Kazuhiro; Shimada, Akira; Asahina, Takayuki; Matsuoka, Kempei [Saiseikai Central Hospital, Tokyo (Japan); Hata, Takashi; Taniyama, Matsuo

1997-07-01

To determine the latent effect of diabetes inheritance on central nervous system, thirty diabetic patients were examined (14 male, 16 female). Seventeen patients had a mother with diabetes, and the other thirteen had non-diabetic mothers. They were previously determined to not have the 3243 mitochondrial tRNA mutation in peripheral leukocytes. Patients were tested for parieto-occipital hypoaccumulation of {sup 123}I-IMP of brain SPECT, a characteristic neurofinding of mitochondrial diabetes mellitus due to the 3243 tRNA mutation. Seven (41.2%) out of 17 subjects with material inheritance had the parieto-occipital abnormality, whereas one (7.7%) out of 13 subjects with non-maternal inheritance had the abnormality. Seventeen (94.4%) out of 18 patients diabetes due to mitochondrial tRNA mutation at position 3243 showed the abnormality. Our results suggest that the material inheritance of diabetes is associated with the hypoaccumulation of {sup 123}I-IMP of brain SPECT. We speculate that, because the patients with maternal inheritance might have subclinical mitochondrial dysfunction due to unknown mitochondrial DNA abnormalities, the mitochondrial DNA abnormality might cause their subclinical brain damage in the parieto-occipital area. (author)

Parieto-occipital hypoaccumulation of 123I-IMP in the brain SPECT associated with maternal inheritance of diabetes mellitus

International Nuclear Information System (INIS)

Suzuki, Yoshihiko; Atsumi, Yoshihito; Hosokawa, Kazuhiro; Shimada, Akira; Asahina, Takayuki; Matsuoka, Kempei; Hata, Takashi; Taniyama, Matsuo.

1997-01-01

To determine the latent effect of diabetes inheritance on central nervous system, thirty diabetic patients were examined (14 male, 16 female). Seventeen patients had a mother with diabetes, and the other thirteen had non-diabetic mothers. They were previously determined to not have the 3243 mitochondrial tRNA mutation in peripheral leukocytes. Patients were tested for parieto-occipital hypoaccumulation of 123 I-IMP of brain SPECT, a characteristic neurofinding of mitochondrial diabetes mellitus due to the 3243 tRNA mutation. Seven (41.2%) out of 17 subjects with material inheritance had the parieto-occipital abnormality, whereas one (7.7%) out of 13 subjects with non-maternal inheritance had the abnormality. Seventeen (94.4%) out of 18 patients diabetes due to mitochondrial tRNA mutation at position 3243 showed the abnormality. Our results suggest that the material inheritance of diabetes is associated with the hypoaccumulation of 123 I-IMP of brain SPECT. We speculate that, because the patients with maternal inheritance might have subclinical mitochondrial dysfunction due to unknown mitochondrial DNA abnormalities, the mitochondrial DNA abnormality might cause their subclinical brain damage in the parieto-occipital area. (author)

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda).

Science.gov (United States)

Kim, Taeho; Kern, Elizabeth; Park, Chungoo; Nadler, Steven A; Bae, Yeon Jae; Park, Joong-Ki

2018-05-10

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

Reversible infantile mitochondrial diseases.

Science.gov (United States)

Boczonadi, Veronika; Bansagi, Boglarka; Horvath, Rita

2015-05-01

Mitochondrial diseases are usually severe and progressive conditions; however, there are rare forms that show remarkable spontaneous recoveries. Two homoplasmic mitochondrial tRNA mutations (m.14674T>C/G in mt-tRNA(Glu)) have been reported to cause severe infantile mitochondrial myopathy in the first months of life. If these patients survive the first year of life by extensive life-sustaining measures they usually recover and develop normally. Another mitochondrial disease due to deficiency of the 5-methylaminomethyl-2-thiouridylate methyltransferase (TRMU) causes severe liver failure in infancy, but similar to the reversible mitochondrial myopathy, within the first year of life these infants may also recover completely. Partial recovery has been noted in some other rare forms of mitochondrial disease due to deficiency of mitochondrial tRNA synthetases and mitochondrial tRNA modifying enzymes. Here we summarize the clinical presentation of these unique reversible mitochondrial diseases and discuss potential molecular mechanisms behind the reversibility. Understanding these mechanisms may provide the key to treatments of potential broader relevance in mitochondrial disease, where for the majority of the patients no effective treatment is currently available.

Transfer RNA species in human lymphocytes stimulated by mitogens and in leukemic cells. [/sup 3/H, /sup 14/C, /sup 32/P tracer techniques

Energy Technology Data Exchange (ETDEWEB)

Griffin, G.D.; Yang, W.K.; Novelli, G.D.

1976-01-01

Transfer ribonucleic acid (tRNA) profiles in human lymphocytes stimulated by various mitogens have been compared with profiles from nonstimulated cells and from leukemic cells using reversed-phase chromatography. Comparisons of (/sup 3/H)- or (/sup 11/C)uridine- or (/sup 32/P)phosphate-labeled tRNAs showed that the greatest changes in tRNA composition upon phytohemagglutinin (PHA) stimulation occurred in the first 8 h after mitogen addition. Stimulation of lymphocytes by pokeweed mitogen, anti-human immunoglobulin, or bacterial lipopolysaccharide resulted in tRNA species which showed distinct differences from each other and also from the tRNAs produced by phytohemagglutinin stimulation. Leukemic lymphocyte tRNAs showed the most extensive differences in profile when compared with chromatograms from non-neoplastic cells stimulated by a variety of mitogens. Specific isoaccepting species of tyrosyl-, aspartyl-, and phenylalanyl-tRNAs were also compared in PHA-stimulated and resting lymphocytes and no differences were found. When these same species were studied in leukemic cells, tyrosyl-tRNA profiles were shifted to elute at a lower salt concentration, while the aspartyl-tRNA profile showed a new peak not present in noncancerous cells.

The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae, a parasitoid wasp of Drosophila

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Daniel S. Oliveira

Full Text Available Abstract The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea, suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

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T Kunisawa

2006-01-01

Full Text Available Complete genomic sequence data are stored in the public GenBank/EMBL/DDBJ databases so that any investigator can make use of the data. This report describes a comparative analysis of codon usage that is impossible without such a public and open data system. A limited number of bacteriophages harbor their own transfer RNAs. Based on a comparison between T4 phage-encoded tRNA species and the relative cellular amounts of host Escherichia coli tRNAs, it is hypothesized that T4 tRNAs could serve to supplement host isoacceptor tRNA species that are present in minor amounts and thus enhance the translational efficiency of phage proteins. When compared to their respective host bacteria, the codon usage data of bacteriophages D3, φC31, HP1, D29 and 933W all show an increased frequency of synonymous codons or amino acids that correspond to phage tRNA species, suggesting their supplemental role in the efficient production of phage proteins. The data-analysis presents an example in which the availability of an open and fully accessible database system would allow one to obtain comprehensive insights into a fundamental problem in molecular biology.

Early steps in protein synthesis and their regulation: a background study related to the biological effects of radiation. Progress report, July 1, 1974--June 30, 1975

International Nuclear Information System (INIS)

Zamecnik, P.C.

1975-01-01

The proposed program is an interwoven effort to study the details of the mechanism of protein synthesis in normal living systems and their alterations in the presence of oncogenic RNA viruses using the avian myeloblastosis virus as a model. Emphasis will be placed on determining the role of the primary structure of the viral RNA and of other factors required for the production of viral proteins in a cell-free system. Continued studies of the initial steps of protein synthesis where much specificity is determined by the tRNA: tRNA synthetase interactions will be carried out using biochemical and genetic techniques. (U.S.)

Complete mitochondrial genome of the giant African snail, Achatina fulica (Mollusca: Achatinidae): a novel location of putative control regions (CR) in the mitogenome within Pulmonate species.

Science.gov (United States)

He, Zhang-Ping; Dai, Xia-Bin; Zhang, Shuai; Zhi, Ting-Ting; Lun, Zhao-Rong; Wu, Zhong-Dao; Yang, Ting-Bao

2016-01-01

The whole sequence (15,057 bp) of the mitochondrial DNA (mtDNA) of the terrestrial snail Achatina fulica (order Stylommatophora) was determined. The mitogenome, as the typical metazoan mtDNA, contains 13 protein-coding genes (PCG), 2 ribosomal RNA genes (rRNA) and 22 transfer RNA genes (tRNA). The tRNA genes include two trnS without standard secondary structure. Interestingly, among the known mitogenomes of Pulmonata species, we firstly characterized an unassigned lengthy sequence (551 bp) between the cox1 and the trnV which may be the CR for the sake of its AT bases usage bias (65.70%) and potential hairpin structure.

AUG is the only initiation codon in eukaryotes

Energy Technology Data Exchange (ETDEWEB)

Sherman, F; McKnight, G; Stewart, J W

1980-01-01

An analysis of mutants of the yeast Saccharomyces cerevisiae indicates that AUG is the sole codon capable of initiating translation of iso-1-cytochrome c. This result with yeast and the sequence results of numerous eukaryotic genes indicate that AUG is the only initiation codon in eukaryotes; in contrast, results with Escherichia colia and bacteriophages indicate that both AUG and GUG are initiation codons in prokaryotes. The difference can be explained by the lack of the t/sup 6/ A hypermodified nucleoside (N-(9-(..beta..-D-ribofuranosyl)purin-6-ylcarbamoyl)threonine) in prokaryotic initiator tRNA and its presence in eukaryotic initiator tRNA.

Healthcare Costs Associated with an Adequate Intake of Sugars, Salt and Saturated Fat in Germany: A Health Econometrical Analysis.

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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.

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.

A test of the cerebellar hypothesis of dyslexia in adequate and inadequate responders to reading intervention.

Science.gov (United States)

Barth, Amy E; Denton, Carolyn A; Stuebing, Karla K; Fletcher, Jack M; Cirino, Paul T; Francis, David J; Vaughn, Sharon

2010-05-01

The cerebellar hypothesis of dyslexia posits that cerebellar deficits are associated with reading disabilities and may explain why some individuals with reading disabilities fail to respond to reading interventions. We tested these hypotheses in a sample of children who participated in a grade 1 reading intervention study (n = 174) and a group of typically achieving children (n = 62). At posttest, children were classified as adequately responding to the intervention (n = 82), inadequately responding with decoding and fluency deficits (n = 36), or inadequately responding with only fluency deficits (n = 56). Based on the Bead Threading and Postural Stability subtests from the Dyslexia Screening Test-Junior, we found little evidence that assessments of cerebellar functions were associated with academic performance or responder status. In addition, we did not find evidence supporting the hypothesis that cerebellar deficits are more prominent for poor readers with "specific" reading disabilities (i.e., with discrepancies relative to IQ) than for poor readers with reading scores consistent with IQ. In contrast, measures of phonological awareness, rapid naming, and vocabulary were strongly associated with responder status and academic outcomes. These results add to accumulating evidence that fails to associate cerebellar functions with reading difficulties.

Detailed NMR, Including 1,1-ADEQUATE, and Anticancer Studies of Compounds from the Echinoderm Colobometra perspinosa

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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.

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

Determining Adequate Averaging Periods and Reference Coordinates for Eddy Covariance Measurements of Surface Heat and Water Vapor Fluxes over Mountainous Terrain

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Yi-Ying Chen Ming-Hsu Li

2012-01-01

Full Text Available Two coordinate rotation approaches (double and planar-fit rotations and no rotation, in association with averaging periods of 15 - 480 min, were applied to compute surface heat and water vapor fluxes using the eddy covariance approach. Measurements were conducted in an experimental watershed, the Lien-Hua-Chih (LHC watershed, located in central Taiwan. For no rotation and double rotation approaches, an adequate averaging period of 15 or 30 min was suggested for better energy closure and small variations on energy closure fractions. For the planar-fit rotation approach, an adequate averaging period of 60 or 120 min was recommended, and a typical averaging period of 30 min is not superior to that of 60 or 120 min in terms of better energy closure and small variations on energy closure fractions. The Ogive function analysis revealed that the energy closure was improved with the increase of averaging time by capturing sensible heat fluxes at low-frequency ranges during certain midday hours at LHC site. Seasonal variations of daily energy closure fractions, high in dry season and low in wet season, were found to be associated with the surface dryness and strength of turbulent development. The mismatching of flux footprint areas among flux sensors was suggested as the cause of larger CF variations during the dry seasons as that indicated by the footprint analysis showing scattered source areas. During the wet season, the underestimation of turbulent fluxes by EC observations at the LHC site was attributed to weak turbulence developments as the source area identified by the footprint analysis was closer to the flux tower than those scattered in dry season.

Emotional Experiences of Obese Women with Adequate Gestational Weight Variation: A Qualitative Study.

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Débora Bicudo Faria-Schützer

Full Text Available 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.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.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.

tRNAGlu increases the affinity of glutamyl-tRNA synthetase for its inhibitor glutamyl-sulfamoyl-adenosine, an analogue of the aminoacylation reaction intermediate glutamyl-AMP: mechanistic and evolutionary implications.

Science.gov (United States)

Blais, Sébastien P; Kornblatt, Jack A; Barbeau, Xavier; Bonnaure, Guillaume; Lagüe, Patrick; Chênevert, Robert; Lapointe, Jacques

2015-01-01

For tRNA-dependent protein biosynthesis, amino acids are first activated by aminoacyl-tRNA synthetases (aaRSs) yielding the reaction intermediates aminoacyl-AMP (aa-AMP). Stable analogues of aa-AMP, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aaRSs. Glutamyl-sulfamoyl-adenosine (Glu-AMS) is the best known inhibitor of Escherichia coli glutamyl-tRNA synthetase (GluRS). Thermodynamic parameters of the interactions between Glu-AMS and E. coli GluRS were measured in the presence and in the absence of tRNA by isothermal titration microcalorimetry. A significant entropic contribution for the interactions between Glu-AMS and GluRS in the absence of tRNA or in the presence of the cognate tRNAGlu or of the non-cognate tRNAPhe is indicated by the negative values of -TΔSb, and by the negative value of ΔCp. On the other hand, the large negative enthalpy is the dominant contribution to ΔGb in the absence of tRNA. The affinity of GluRS for Glu-AMS is not altered in the presence of the non-cognate tRNAPhe, but the dissociation constant Kd is decreased 50-fold in the presence of tRNAGlu; this result is consistent with molecular dynamics results indicating the presence of an H-bond between Glu-AMS and the 3'-OH oxygen of the 3'-terminal ribose of tRNAGlu in the Glu-AMS•GluRS•tRNAGlu complex. Glu-AMS being a very close structural analogue of Glu-AMP, its weak binding to free GluRS suggests that the unstable Glu-AMP reaction intermediate binds weakly to GluRS; these results could explain why all the known GluRSs evolved to activate glutamate only in the presence of tRNAGlu, the coupling of glutamate activation to its transfer to tRNA preventing unproductive cleavage of ATP.

Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes in Toxoplasma gondii.

Science.gov (United States)

Padgett, Leah R; Lentini, Jenna M; Holmes, Michael J; Stilger, Krista L; Fu, Dragony; Sullivan, William J

2018-01-01

Radical S-adenosylmethionine (rSAM) enzymes use a 5'-deoxyadensyl 5'-radical to methylate a wide array of diverse substrates including proteins, lipids and nucleic acids. One such enzyme, Elongator protein-3 (TgElp3), is an essential protein in Toxoplasma gondii, a protozoan parasite that can cause life-threatening opportunistic disease. Unlike Elp3 homologues which are present in all domains of life, TgElp3 localizes to the outer mitochondrial membrane (OMM) via a tail-anchored trafficking mechanism in Toxoplasma. Intriguingly, we identified a second tail-anchored rSAM domain containing protein (TgRlmN) that also localizes to the OMM. The transmembrane domain (TMD) on Toxoplasma Elp3 and RlmN homologues is required for OMM localization and has not been seen beyond the chromalveolates. Both TgElp3 and TgRlmN contain the canonical rSAM amino acid sequence motif (CxxxCxxC) necessary to form the 4Fe-4S cluster required for tRNA modifications. In E. coli, RlmN is responsible for the 2-methlyadenosine (m2A) synthesis at purine 37 in tRNA while in S. cerevisiae, Elp3 is necessary for the formation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at the wobble tRNA position. To investigate why these two rSAM enzymes localize to the mitochondrion in Toxoplasma, and whether or not TgRlmN and TgElp3 possess tRNA methyltransferase activity, a series of mutational and biochemical studies were performed. Overexpression of either TgElp3 or TgRlmN resulted in a significant parasite replication defect, but overexpression was tolerated if either the TMD or rSAM domain was mutated. Furthermore, we show the first evidence that Toxoplasma tRNAGlu contains the mcm5s2U modification, which is the putative downstream product generated by TgElp3 activity.

Liver conversion of docosahexaenoic and arachidonic acids from their 18-carbon precursors in rats on a DHA-free but α-LNA-containing n-3 PUFA adequate diet.

Science.gov (United States)

Gao, Fei; Kim, Hyung-Wook; Igarashi, Miki; Kiesewetter, Dale; Chang, Lisa; Ma, Kaizong; Rapoport, Stanley I

2011-01-01

The long-chain polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid (EPA, 20:5n-3), docosahexaenoic acid (DHA, 22:6n-3), and arachidonic acid (AA, 20:4n-6), are critical for health. These PUFAs can be synthesized in liver from their plant-derived precursors, α-linolenic acid (α-LNA, 18:3n-3) and linoleic acid (LA, 18:2n-6). Vegetarians and vegans may have suboptimal long-chain n-3 PUFA status, and the extent of the conversion of α-LNA to EPA and DHA by the liver is debatable. We quantified liver conversion of DHA and other n-3 PUFAs from α-LNA in rats fed a DHA-free but α-LNA (n-3 PUFA) adequate diet, and compared results to conversion of LA to AA. [U-(13)C]LA or [U-(13)C]α-LNA was infused intravenously for 2h at a constant rate into unanesthetized rats fed a DHA-free α-LNA adequate diet, and published equations were used to calculate kinetic parameters. The conversion coefficient k(⁎) of DHA from α-LNA was much higher than for AA from LA (97.2×10(-3) vs. 10.6×10(-3)min(-1)), suggesting that liver elongation-desaturation is more selective for n-3 PUFA biosynthesis on a per molecule basis. The net daily secretion rate of DHA, 20.3μmol/day, exceeded the reported brain DHA consumption rate by 50-fold, suggesting that the liver can maintain brain DHA metabolism with an adequate dietary supply solely of α-LNA. This infusion method could be used in vegetarians or vegans to determine minimal daily requirements of EPA and DHA in humans. Published by Elsevier B.V.

Exploring barriers to and enablers of adequate healthcare for Indigenous Australian prisoners with cancer: a scoping review drawing on evidence from Australia, Canada and the United States.

Science.gov (United States)

Olds, Jessica; Reilly, Rachel; Yerrell, Paul; Stajic, Janet; Micklem, Jasmine; Morey, Kim; Brown, Alex

International frameworks supported by national principles in Australia stipulate that prisoners should be provided with health services equivalent to those provided in the general community. However, a number of barriers unique to the prison system may hinder the provision of equitable healthcare for this population. In Australia, Indigenous people carry a greater burden of cancer mortality, which the Cancer Data and Aboriginal Disparities (CanDAD) project is seeking to address. During the course of recruiting participants to the CanDAD study, Indigenous Australian prisoners with cancer emerged as an important, under-researched but difficult to access sub-group. This scoping review sought to identify barriers and facilitators of access to adequate and equitable healthcare for Indigenous Australian prisoners with cancer in Australia. This review demonstrated a lack of research and, as such, the scoping review was extended to prisoners with cancer in Australia, New Zealand, the United States and Canada. This approach was taken in order to summarise the existing body of evidence regarding the barriers and facilitators of access to adequate and equitable healthcare for those who are incarcerated and suffering from cancer, and highlight areas that may require further investigation. Eight studies or commentaries were found to meet the inclusion criteria. This limited set of findings pointed to a range of possible barriers faced by prisoners with cancer, including a tension between the prisons' concern with security versus the need for timely access to medical care. Findings identified here offer potential starting points for research and policy development. Further research is needed to better elucidate how barriers to adequate cancer care for prisoners may be identified and overcome, in Australia and internationally. Furthermore, given Indigenous Australians' over-burden of cancer mortality and over-representation in the prison system, further research is needed to

Fair Balance and Adequate Provision in Direct-to-Consumer Prescription Drug Online Banner Advertisements: A Content Analysis

Science.gov (United States)

2016-01-01

Background The current direct-to-consumer advertising (DTCA) guidelines were developed with print, television, and radio media in mind, and there are no specific guidelines for online banner advertisements. Objective This study evaluates how well Internet banner ads comply with existing Food and Drug Administration (FDA) guidelines for DTCA in other media. Methods A content analysis was performed of 68 banner advertisements. A coding sheet was developed based on (1) FDA guidance documents for consumer-directed prescription drug advertisements and (2) previous DTCA content analyses. Specifically, the presence of a brief summary detailing the drug’s risks and side effects or of a “major statement” identifying the drug’s major risks, and the number and type of provisions made available to consumers for comprehensive information about the drug were coded. In addition, the criterion of “fair balance,” the FDA’s requirement that prescription drug ads balance information relating to the drug’s risks with information relating to its benefits, was measured by numbering the benefit and risk facts identified in the ads and by examining the presentation of risk and benefit information. Results Every ad in the sample included a brief summary of risk information and at least one form of adequate provision as required by the FDA for broadcast ads that do not give audiences a brief summary of a drug’s risks. No ads included a major statement. There were approximately 7.18 risk facts for every benefit fact. Most of the risks (98.85%, 1292/1307) were presented in the scroll portion of the ad, whereas most of the benefits (66.5%, 121/182) were presented in the main part of the ad. Out of 1307 risk facts, 1292 were qualitative and 15 were quantitative. Out of 182 benefit facts, 181 were qualitative and 1 was quantitative. The majority of ads showed neutral images during the disclosure of benefit and risk facts. Only 9% (6/68) of the ads displayed positive images and

Fair Balance and Adequate Provision in Direct-to-Consumer Prescription Drug Online Banner Advertisements: A Content Analysis.

Science.gov (United States)

Adams, Crystal

2016-02-18

The current direct-to-consumer advertising (DTCA) guidelines were developed with print, television, and radio media in mind, and there are no specific guidelines for online banner advertisements. This study evaluates how well Internet banner ads comply with existing Food and Drug Administration (FDA) guidelines for DTCA in other media. A content analysis was performed of 68 banner advertisements. A coding sheet was developed based on (1) FDA guidance documents for consumer-directed prescription drug advertisements and (2) previous DTCA content analyses. Specifically, the presence of a brief summary detailing the drug's risks and side effects or of a "major statement" identifying the drug's major risks, and the number and type of provisions made available to consumers for comprehensive information about the drug were coded. In addition, the criterion of "fair balance," the FDA's requirement that prescription drug ads balance information relating to the drug's risks with information relating to its benefits, was measured by numbering the benefit and risk facts identified in the ads and by examining the presentation of risk and benefit information. Every ad in the sample included a brief summary of risk information and at least one form of adequate provision as required by the FDA for broadcast ads that do not give audiences a brief summary of a drug's risks. No ads included a major statement. There were approximately 7.18 risk facts for every benefit fact. Most of the risks (98.85%, 1292/1307) were presented in the scroll portion of the ad, whereas most of the benefits (66.5%, 121/182) were presented in the main part of the ad. Out of 1307 risk facts, 1292 were qualitative and 15 were quantitative. Out of 182 benefit facts, 181 were qualitative and 1 was quantitative. The majority of ads showed neutral images during the disclosure of benefit and risk facts. Only 9% (6/68) of the ads displayed positive images and none displayed negative images when presenting risks

The mitochondrial genome of the deep-sea glass sponge Lophophysema eversa (Porifera, Hexacinellida, Hyalonematidae).

Science.gov (United States)

Zhang, Yanjie; Sun, Jin; Li, Xinzheng; Qiu, Jian-Wen

2016-01-01

We reported a nearly complete mitochondrial genome (mitogenome) from the glass sponge Lophophysema eversa, the second mitogenome in the order Amphidiscosida and the ninth in the class Hexactinellida. It is 20,651 base pairs in length and contains 39 genes including 13 protein-coding genes, 2 ribosomal RNA subunit genes and 24 tRNA genes. The gene content and order of L. eversa are identical to those of Tabachnickia sp., the other species with a sequenced mitogenome in Amphidiscosida, except with two additional tRNAs and three tRNA translocations. The cob gene has a +1 translational frameshift. These results will contribute to a better understanding of the phylogeny of glass sponges.

Synthesis and biological incorporatin of icons into macromolecules for NMR study

International Nuclear Information System (INIS)

Grant, D.M.

1976-02-01

Work has proceeded successfully to synthesize novel 13 C-labeled materials for incorporation into macromolecules. Gram quantities of C-4 labeled uracil have been synthesized and incorporated, by means of a mutant bacterial strain into t-RNA. The t-RNA has been isolated, purified, and carbon-13 T 1 studies have begun. A modern, well equipped biochemistry laboratory has become functional during the present contract period. Good progress has been made on nonenzymatic reactions of pyridoxal-5'-phosphate with selected amino actions. This effort has successfully elucidated many reaction intermediates and products. In addition, 13 C containing haptens have been synthesized and screening tests have now begun on rabbits to verify the specificity of antibodies for two haptens

Towards a sustainable architecture: Adequate to the environment and of maximum energy efficiency; Hacia una arquitectura sustentable: adecuada al ambiente y de maxima eficiencia energetica

Energy Technology Data Exchange (ETDEWEB)

Morillon Galvez, David [Comision Nacional para el Ahorro de Energia, Mexico, D. F. (Mexico)

1999-07-01

An analysis of the elements and factors that the architecture of buildings must have to be sustainable, such as: a design adequate to the environment, saving and efficient use of alternate energies, and the auto-supply is presented. In addition a methodology for the natural air conditioning (bioclimatic architecture) of buildings, as well as ideas for the saving and efficient use of energy, with the objective of contributing to the adequate use of components of the building (walls, ceilings, floors etc.), is presented, that when interacting with the environment it takes advantage of it, without deterioration of the same, obtaining energy efficient designs. [Spanish] Se presenta un analisis de los elementos y factores que debe tener la arquitectura de edificios para ser sustentable, como; un diseno adecuado al ambiente, ahorro y uso eficiente de la energia, el uso de energias alternas y el autoabastecimiento. Ademas se propone una metodologia para la climatizacion natural (arquitectura bioclimatica) de edificios, asi como ideas para el ahorro y uso eficiente de energia, con el objetivo de aportar al uso adecuado de componentes del edificio (muros, techos, pisos etc.) que al interactuar con el ambiente tome ventaja de el, sin deterioro del mismo, logrando disenos energeticamente eficientes.

Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae).

Science.gov (United States)

Jiang, Shao-Tong; Hong, Gui-Yun; Yu, Miao; Li, Na; Yang, Ying; Liu, Yan-Qun; Wei, Zhao-Jun

2009-05-22

The complete mitochondrial genome (mitogenome) of Eriogyna pyretorum (Lepidoptera: Saturniidae) was determined as being composed of 15,327 base pairs (bp), including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The arrangement of the PCGs is the same as that found in the other sequenced lepidopteran. The AT skewness for the E. pyretorum mitogenome is slightly negative (-0.031), indicating the occurrence of more Ts than As. The nucleotide composition of the E. pyretorum mitogenome is also biased toward A + T nucleotides (80.82%). All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 and 2 (cox1 and cox2). Two of the 13 PCGs harbor the incomplete termination codon by T. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1(AGN) and trnS2(UCN). Phylogenetic analysis among the available lepidopteran species supports the current morphology-based hypothesis that Bombycoidea, Geometroidea, Notodontidea, Papilionoidea and Pyraloidea are monophyletic. As has been previously suggested, Bombycidae (Bombyx mori and Bombyx mandarina), Sphingoidae (Manduca sexta) and Saturniidae (Antheraea pernyi, Antheraea yamamai, E. pyretorum and Caligula boisduvalii) formed a group.

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae).

Science.gov (United States)

Chen, Long; Chen, Peng-Yan; Xue, Xiao-Feng; Hua, Hai-Qing; Li, Yuan-Xi; Zhang, Fan; Wei, Shu-Jun

2018-05-04

Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.

Pakistan: the new target of terrorism. Are Karachi's emergency medical response systems adequately prepared?

Science.gov (United States)

Siddiqui, Muhammad Ahmed; Jawad, Ahmed; Minhas, Saeed; Ansari, Asma; Siddiqui, Afrah; Mehtab, Sana

2009-07-01

To assess the efficacy and preparedness of the pre-hospital and hospital emergency medical systems and post graduate trainees in the city to deal with a massive terrorist strike. A cross-sectional survey of postgraduate trainees was conducted at Jinnah Postgraduate Medical Center and Civil Hospital Karachi from 21st July 2007 to 24th July 2007, to evaluate the preparedness and self identified deficiencies of doctors involved in massive trauma casualty management. To assess the pre-hospital care in Karachi, structured telephonic interviews were conducted of administrators of two private run charity based ambulance services. Out of the 90 respondents questioned regarding a self assessment of their training, only 3 (3.3%) of them were confident about their management of bomb blast victims. Eighty-seven (96.6%) of the respondents felt they required some further training (44.4%) or comprehensive training (52.2%). No simulated drills or courses had been conducted for disaster management in the emergency department of the surveyed Hospitals. Most of the ambulance drivers had no paramedic training. Ambulances are equipped with a stretcher and an oxygen cylinder only. No resuscitation measures are available in the ambulances. With an increasing number of terrorist attacks in the country, massive influx of casualties in a relatively short time span has become a regular feature of the Pakistani hospital system. Lack of adequate training at pre-hospital and in hospital levels may translate into increasing morbidities and mortalities. It is imperative that training of junior doctors and paramedical staff be conducted regularly and an effective regional communication base established for efficient interdepartmental coordination.

Milk vitamin D in relation to the 'adequate intake' for 0-6-month-old infants : A study in lactating women with different cultural backgrounds, living at different latitudes

NARCIS (Netherlands)

Stoutjesdijk, Eline; Schaafsma, Anne; Nhien, Nguyen V.; Khor, Geok Lin; Kema, Ido P.; Hollis, Bruce W.; Dijck-Brouwer, D. A. Janneke; Muskiet, Frits A. J.

2017-01-01

Breast-fed infants are susceptible to vitamin D deficiency rickets. The current vitamin D adequate intake' (AI) for 0-6-month-old infants is 10 mu g/d, corresponding with a human milk antirachitic activity (ARA) of 513 IU/l. We were particularly interested to see whether milk ARA of mothers with

DO FINANCIAL STATEMENTS PROVIDE ADEQUATE INFORMATION ABOUT THE CAPITALIZATION OF COSTS RELATED TO INTANGIBLE ASSETS?: AN EMPIRICAL RESEARCH ON ITALIAN LISTED COMPANIES

Directory of Open Access Journals (Sweden)

Stefania Vignini

2015-11-01

Full Text Available 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 process and the cost control, thus guaranteeing the verifiability and representational faithfulness of the information disclosed. This paper is an empirical analysis and is concerned to investigate the financial statements of 250 Italian listed companies.

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

Now you see it. Now you don't: fair balance and adequate provision in advertisements for drugs before and after the switch from prescription to over-the-counter.

Science.gov (United States)

Faerber, Adrienne E; Kreling, David H

2012-01-01

The objective of this study was to measure differences in fair balance (benefit and risk statements) and adequate provision (toll-free numbers, Internet URLs, print ad references, and medical professional references) in advertising content for drugs that have switched from prescription to over-the-counter (OTC). The Vanderbilt TV News Archive was used to select products to study, to measure the frequency and placement of ads for those products, and to view advertising content for those products. Unique advertisements (n = 108) for loratadine (Claritin), citirizine (Zyrtec), and omeprazole (Prilosec) were analyzed for the presence of adequate provision statements and for the frequency of benefit, risk, and other statements. OTC ads were shorter than prescription ads by 10.6 seconds but contained the same total number of statements. Most prescription ads (n (RX) = 31) contained toll-free numbers (97%), Internet URLs (94%), medical professional references (100%) and print ad references (68%). Few OTC ads (n (OTC) = 77) contained adequate provision statements: 4% contained toll-free numbers and 10% contained Internet URLs. Prescription ads had similar numbers of benefits (1.5) and risks (1.8) per 30 seconds of ad time, and OTC ads had more benefits (6.6) than risks (1.2) per 30 seconds of ad time. Prescription drug ads contained risk statements that listed specific side effects and explicit harms from taking the product, but OTC ads contained nonspecific risk information and statements that implied risk rather than directly identifying risk. Differences in the Food and Drug Administration (FDA) and Federal Trade Commission (FTC) regulation of advertising affected the balance of risk and benefit information that appeared and the specificity of risk information available.

Are current practices adequate

International Nuclear Information System (INIS)

Taylor, T.B.

1975-01-01

Events related to safeguards during the last year are reviewed. Present needs are a clear statement of safeguards objectives, more Federal funds, and design of facilities for easier safeguards. It is felt that effective safeguards can be implemented at relatively low overall cost to industry. C. Walske's presentation of the AIF position is strongly endorsed. (U.S.)

Are uranium reserves adequate?

International Nuclear Information System (INIS)

Anon.

2006-01-01

Against a backdrop of growing concerns about global warming and geopolitical pressures on fossil energies, especially natural gas and oil, interest in nuclear power has revived considerably. Conscious of its addiction to oil and reeling from a series of gigantic blackouts, the United States, in the words of its president, must 'aggressively move forward with the construction of nuclear power plants'. Some European countries have approved new power plant construction (Finland and France), while the more reserved ones (Belgium, Germany and Sweden) have begun to show a change in attitude. Asia, meanwhile, is host to the planet's largest number of potential nuclear construction projects in this first half of the 21. century. All these signs point to a sharp rise in uranium consumption, the basic fuel for these plants. But are there enough resources to support a nuclear revival on a planetary scale? The publication of the Red Book on uranium in late May 2006 was an opportunity for Thierry Dujardin, Deputy Director of Science and Development at the OECD's Nuclear Energy Agency, to take stock of resources. He gives his opinion in this paper

access to adequate housing

African Journals Online (AJOL)

Nicola Smit

chauffeurs and restaurant/hotel workers approached the Development Action ..... 10 Ibid. 11 Budget speech by LN Sisulu, Minister of Housing, 28 May 2008, available at .... exorbitantly high property prices in the Cape Town CBD and environs, ...

Making ecological models adequate

Science.gov (United States)

Getz, Wayne M.; Marshall, Charles R.; Carlson, Colin J.; Giuggioli, Luca; Ryan, Sadie J.; Romañach, Stephanie; Boettiger, Carl; Chamberlain, Samuel D.; Larsen, Laurel; D'Odorico, Paolo; O'Sullivan, David

2018-01-01

Critical evaluation of the adequacy of ecological models is urgently needed to enhance their utility in developing theory and enabling environmental managers and policymakers to make informed decisions. Poorly supported management can have detrimental, costly or irreversible impacts on the environment and society. Here, we examine common issues in ecological modelling and suggest criteria for improving modelling frameworks. An appropriate level of process description is crucial to constructing the best possible model, given the available data and understanding of ecological structures. Model details unsupported by data typically lead to over parameterisation and poor model performance. Conversely, a lack of mechanistic details may limit a model's ability to predict ecological systems’ responses to management. Ecological studies that employ models should follow a set of model adequacy assessment protocols that include: asking a series of critical questions regarding state and control variable selection, the determinacy of data, and the sensitivity and validity of analyses. We also need to improve model elaboration, refinement and coarse graining procedures to better understand the relevancy and adequacy of our models and the role they play in advancing theory, improving hind and forecasting, and enabling problem solving and management.

Biodiversity of the Great Barrier Reef—how adequately is it protected?

Directory of Open Access Journals (Sweden)

Zoe T. Richards

2018-05-01

Full Text Available Background The Great Barrier Reef (GBR is the world’s most iconic coral reef ecosystem, recognised internationally as a World Heritage Area of outstanding significance. Safeguarding the biodiversity of this universally important reef is a core legislative objective; however, ongoing cumulative impacts including widespread coral bleaching and other detrimental impacts have heightened conservation concerns for the future of the GBR. Methods Here we review the literature to report on processes threatening species on the GBR, the status of marine biodiversity, and evaluate the extent of species-level monitoring and reporting. We assess how many species are listed as threatened at a global scale and explore whether these same species are protected under national threatened species legislation. We conclude this review by providing future directions for protecting potentially endangered elements of biodiversity within the GBR. Results Most of the threats identified to be harming the diversity of marine life on the GBR over the last two–three decades remain to be effectively addressed and many are worsening. The inherent resilience of this globally significant coral reef ecosystem has been seriously compromised and various elements of the biological diversity for which it is renowned may be at risk of silent extinction. We show at least 136 of the 12,000+ animal species known to occur on the GBR (approximately 20% of the 700 species assessed by the IUCN occur in elevated categories of threat (Critically Endangered, Endangered or Vulnerable at a global scale. Despite the wider background level of threat for these 136 species, only 23 of them are listed as threatened under regional or national legislation. Discussion To adequately protect the biodiversity values of the GBR, it may be necessary to conduct further targeted species-level monitoring and reporting to complement ecosystem management approaches. Conducting a vigorous value of information

Capillary PO2 does not adequately reflect arterial PO2 in hypoxemic COPD patients.

Science.gov (United States)

Magnet, Friederike Sophie; Majorski, Daniel Sebastian; Callegari, Jens; Schwarz, Sarah Bettina; Schmoor, Claudia; Windisch, Wolfram; Storre, Jan Hendrik

2017-01-01

To compare arterial (P a O 2 ) with capillary (P c O 2 ) partial pressure of oxygen in hypoxemic COPD patients because capillary blood gas analysis (CBG) is increasingly being used as an alternative to arterial blood gas analysis (ABG) in a non-intensive care unit setting, although the agreement between P c O 2 and P a O 2 has not been evaluated in hypoxemic COPD patients. Bland-Altman comparison of P a O 2 and P c O 2 served as the primary outcome parameter if P c O 2 values were ≤60 mmHg and the secondary outcome parameter if P c O 2 values were ≤55 mmHg. Pain associated with the measurements was assessed using a 100-mm visual analog scale. One hundred and two P a O 2 /P c O 2 measurement pairs were obtained. For P c O 2 values ≤60 mmHg, the mean difference between P a O 2 and P c O 2 was 5.99±6.05 mmHg (limits of agreement: -5.88 to 17.85 mmHg). For P c O 2 values ≤55 mmHg (n=73), the mean difference was 5.33±5.52 mmHg (limits of agreement: -5.48 to 16.15 mmHg). If P a O 2 ≤55 (≤60) mmHg was set as the cut-off value, in 20.6% (30.4%) of all patients, long-term oxygen therapy have been unnecessarily prescribed if only P c O 2 would have been assessed. ABG was rated as more painful compared with CBG. P c O 2 does not adequately reflect P a O 2 in hypoxemic COPD patients, which can lead to a relevant number of unnecessary long-term oxygen therapy prescriptions.

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

Do immigrants from Turkey, Pakistan and Yugoslavia receive adequate medical treatment with beta-blockers and statins after acute myocardial infarction compared with Danish-born residents? A register-based follow-up study

DEFF Research Database (Denmark)

Hempler, Nana Folmann; Diderichsen, Finn; Larsen, Finn Breinholt

2010-01-01

We undertook a study investigating whether immigrants from Turkey, Pakistan and Yugoslavia received adequate medical treatment with beta-blockers and statins after acute myocardial infarction (AMI) when compared with Danish-born residents and explored whether associations between patient origin...

Mapping Escherichia coli elongation factor Tu residues involved in binding of aminoacyl-tRNA

DEFF Research Database (Denmark)

Wiborg, Ove; Andersen, C; Knudsen, Charlotte Rohde

1996-01-01

Two residues of Escherichia coli elongation factor Tu involved in binding of aminoacyl-tRNA were identified and subjected to mutational analysis. Lys-89 and Asn-90 were each replaced by either Ala or Glu. The four single mutants were denoted K89A, K89E, N90A, and N90E, respectively. The mutants...... were characterized with respect to thermal and chemical stability, GTPase activity, tRNA affinity, and activity in an in vitro translation assay. Most conspicuously tRNA affinities were reduced for all mutants. The results verify our structural analysis of elongation factor Tu in complex with aminoacyl....... Their functional roles are discussed in relation to the structure of elongation factor Tu in complex with aminoacyl-tRNA. Udgivelsesdato: 1996-Aug-23...

The complete mitochondrial genome of the redeye mullet Liza haematocheila (Teleostei, Mugilidae).

Science.gov (United States)

Chen, Jianhua; Li, Yinglei; Chen, Haigang; Yan, Binlun; Meng, Xueping

2015-01-01

The complete mitochondrial sequence of the redeye mullet Liza haematocheila has been determined. The circle genome is 16,822 bp in size, and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of L. haematocheila was similar to that of most other teleosts. The base composition of H-strand is 26.42% (A), 26.38% (T), 16.72% (G) and 30.47% (C), with an AT content of 52.8%. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of L. haematocheila presented will be in favor of resolving phylogenetic relationships within the family Scatophagidae and the Mugiliformes.

Functions and cellular localization of cysteine desulfurase and selenocysteine lyase in Trypanosoma brucei

Czech Academy of Sciences Publication Activity Database

Poliak, Pavel; Van Hoewyk, D.; Oborník, Miroslav; Zíková, Alena; Stuart, K. D.; Tachezy, J.; Pilon, M.; Lukeš, Julius

2010-01-01

Roč. 277, č. 2 (2010), s. 383-393 ISSN 1742-464X R&D Projects: GA ČR GA204/09/1667 Institutional research plan: CEZ:AV0Z60220518 Keywords : Fe–S cluster * mitochondrion * RNAi * selenoprotein * Trypanosoma Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.129, year: 2010

InterProScan Result: FS925326 [KAIKOcDNA[Archive

Lifescience Database Archive (English)

Full Text Available ine/other tRNA-ribosyltransferase Biological Process: tRNA modification (GO:0006400)|Molecular Function: que...uine tRNA-ribosyltransferase activity (GO:0008479)|Biological Process: queuosine biosynthetic process (GO:0008616) ...

Loss of the RNA polymerase III repressor MAF1 confers obesity resistance.

Science.gov (United States)

Bonhoure, Nicolas; Byrnes, Ashlee; Moir, Robyn D; Hodroj, Wassim; Preitner, Frédéric; Praz, Viviane; Marcelin, Genevieve; Chua, Streamson C; Martinez-Lopez, Nuria; Singh, Rajat; Moullan, Norman; Auwerx, Johan; Willemin, Gilles; Shah, Hardik; Hartil, Kirsten; Vaitheesvaran, Bhavapriya; Kurland, Irwin; Hernandez, Nouria; Willis, Ian M

2015-05-01

MAF1 is a global repressor of RNA polymerase III transcription that regulates the expression of highly abundant noncoding RNAs in response to nutrient availability and cellular stress. Thus, MAF1 function is thought to be important for metabolic economy. Here we show that a whole-body knockout of Maf1 in mice confers resistance to diet-induced obesity and nonalcoholic fatty liver disease by reducing food intake and increasing metabolic inefficiency. Energy expenditure in Maf1(-/-) mice is increased by several mechanisms. Precursor tRNA synthesis was increased in multiple tissues without significant effects on mature tRNA levels, implying increased turnover in a futile tRNA cycle. Elevated futile cycling of hepatic lipids was also observed. Metabolite profiling of the liver and skeletal muscle revealed elevated levels of many amino acids and spermidine, which links the induction of autophagy in Maf1(-/-) mice with their extended life span. The increase in spermidine was accompanied by reduced levels of nicotinamide N-methyltransferase, which promotes polyamine synthesis, enables nicotinamide salvage to regenerate NAD(+), and is associated with obesity resistance. Consistent with this, NAD(+) levels were increased in muscle. The importance of MAF1 for metabolic economy reveals the potential for MAF1 modulators to protect against obesity and its harmful consequences. © 2015 Bonhoure et al.; Published by Cold Spring Harbor Laboratory Press.

A double base change in alternate base pairs induced by ultraviolet irradiation in a glycine transfer RNA gene

International Nuclear Information System (INIS)

Coleman, R.D.; Dunst, R.W.; Hill, C.W.; Pennsylvania State Univ., Hershey

1980-01-01

The glyUsusub(AGA) mutation affects Escherichia coli tRNAsup(Gly)sub(GGG), changing it to an AGA missense suppressor tRNA. Sequence studies have shown that the mutation involves a double base substitution at the first and third positions of the tRNA anticodon, the result being a change in the anticodon from CCC to UCU. A system has been developed to facilitate the detection of this novel mutation, and we have shown that ultraviolet irradiation and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) are effective in causing the double base change. A single observation of the mutation occuring spontaneously has been made also. The frequency of MNNG-induced glyUsusub(AGA) mutations is compatible with their being caused by two separate mutagenic events. The frequency of UV-induced glyUsusub(AGA) mutations, however, strongly suggests that the occurence of one base substitution strongly enhances the chance of finding the second substitution at the alternate position. In addition to the double change in the anticodon, the glyUsusub(AGA) tRNA differs from tRNAsup(gly)sub(GGG) in that it bears a modification of the A adjacent to the 3' position of the anticodon. Most likely, this modified base is N-[9-(β-D-ribofuranosyl)-purin-6-ylcarbamoyl] threonine. (orig.) 891 AJ/orig. 892 BRE [de

Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus

International Nuclear Information System (INIS)

Pleshe, Elizabeth; Truesdell, John; Batey, Robert T.

2005-01-01

The crystal structure of Aquifex aeolicus TrmH, a member of the a/b-knot superfamily responsible for O methylation of G18 of tRNAs, was determined to 1.85 Å resolution using the molecular-replacement method. Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2′-hydroxyl group of the ribose sugar, which is performed by a number of S-adenosylmethionine (SAM) dependent methyltransferases. In bacteria, many of these modifications in tRNA and rRNA are carried out by the α/β-knot superfamily of enzymes, whose SAM-binding pocket is created by a characteristic deep trefoil knot. TrmH, an enzyme found throughout all three kingdoms of life, modifies the universally conserved guanosine 18 position of tRNA. The crystal structure of TrmH from the thermophilic bacterium Aquifex aeolicus has been determined at 1.85 Å resolution using data collected from a synchrotron-radiation source. The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the α/β-knot superfamily, with α-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding

Gene arrangement and sequence of mitochondrial genomes yield insights into the phylogeny and evolution of bees and sphecid wasps (Hymenoptera: Apoidea).

Science.gov (United States)

Zheng, Bo-Ying; Cao, Li-Jun; Tang, Pu; van Achterberg, Kees; Hoffmann, Ary A; Chen, Hua-Yan; Chen, Xue-Xin; Wei, Shu-Jun

2018-07-01

The Apoidea represent a large and common superfamily of the Hymenoptera including the bees and sphecid wasps. A robust phylogenetic tree is essential to understanding the diversity, taxonomy and evolution of the Apoidea. In this study, features of apoid mitochondrial genomes were used to reconstruct phylogenetic relationships. Twelve apoid mitochondrial genomes were newly sequenced, representing six families and nine subfamilies. Gene rearrangement events have occurred in all apoid mitochondrial genomes sequenced to date. Sphecid wasps have both tRNA and protein-coding gene rearrangements in 5 of 8 species. In bees, the only rearranged genes are tRNAs; long-tongued bees (Apidae + Megachilidae) are characterized by movement of trnA to the trnI-trnQ-trnM tRNA cluster. Phylogenetic analyses of mitochondrial gene sequences support the known paraphyly of sphecid wasps, with bees nested within this clade. The Ampulicidae is sister to the remaining Apoidea. Crabronidae is paraphyletic, split into Crabronidae s.s. and Philanthidae, with the latter group a sister clade to bees. The monophyletic bees are either classified into two clades, long-tongued bees (Apidae + Megachilidae) and short-tongued bees (Andrenidae + Halictidae + Colletidae + Melitidae), or three groups with the Melitidae sister to the other bees. Our study showed that both gene sequences and arrangements provide information on the phylogeny of apoid families. Copyright © 2018 Elsevier Inc. All rights reserved.

Multiple RNA processing defects and impaired chloroplast function in plants deficient in the organellar protein-only RNase P enzyme.

Directory of Open Access Journals (Sweden)

Wenbin Zhou

Full Text Available Transfer RNA (tRNA precursors undergo endoribonucleolytic processing of their 5' and 3' ends. 5' cleavage of the precursor transcript is performed by ribonuclease P (RNase P. While in most organisms RNase P is a ribonucleoprotein that harbors a catalytically active RNA component, human mitochondria and the chloroplasts (plastids and mitochondria of seed plants possess protein-only RNase P enzymes (PRORPs. The plant organellar PRORP (PRORP1 has been characterized to some extent in vitro and by transient gene silencing, but the molecular, phenotypic and physiological consequences of its down-regulation in stable transgenic plants have not been assessed. Here we have addressed the function of the dually targeted organellar PRORP enzyme in vivo by generating stably transformed Arabidopsis plants in which expression of the PRORP1 gene was suppressed by RNA interference (RNAi. PRORP1 knock-down lines show defects in photosynthesis, while mitochondrial respiration is not appreciably affected. In both plastids and mitochondria, the effects of PRORP1 knock-down on the processing of individual tRNA species are highly variable. The drastic reduction in the levels of mature plastid tRNA-Phe(GAA and tRNA-Arg(ACG suggests that these two tRNA species limit plastid gene expression in the PRORP1 mutants and, hence, are causally responsible for the mutant phenotype.

Is the Health of Irish Workers adequately protected from the effects Radon Gas?

International Nuclear Information System (INIS)

Heery Mary

2006-08-01

prosecuted for failing to comply with this legislation. Hence, the health of Irish workers is not being adequately protected from the effects of this silent killer, radon gas

Defining an adequate sample of earlywood vessels for retrospective injury detection in diffuse-porous species.

Directory of Open Access Journals (Sweden)

Estelle Arbellay

Full Text Available Vessels of broad-leaved trees have been analyzed to study how trees deal with various environmental factors. Cambial injury, in particular, has been reported to induce the formation of narrower conduits. Yet, little or no effort has been devoted to the elaboration of vessel sampling strategies for retrospective injury detection based on vessel lumen size reduction. To fill this methodological gap, four wounded individuals each of grey alder (Alnus incana (L. Moench and downy birch (Betula pubescens Ehrh. were harvested in an avalanche path. Earlywood vessel lumina were measured and compared for each tree between the injury ring built during the growing season following wounding and the control ring laid down the previous year. Measurements were performed along a 10 mm wide radial strip, located directly next to the injury. Specifically, this study aimed at (i investigating the intra-annual duration and local extension of vessel narrowing close to the wound margin and (ii identifying an adequate sample of earlywood vessels (number and intra-ring location of cells attesting to cambial injury. Based on the results of this study, we recommend analyzing at least 30 vessels in each ring. Within the 10 mm wide segment of the injury ring, wound-induced reduction in vessel lumen size did not fade with increasing radial and tangential distances, but we nevertheless advise favoring early earlywood vessels located closest to the injury. These findings, derived from two species widespread across subarctic, mountainous, and temperate regions, will assist retrospective injury detection in Alnus, Betula, and other diffuse-porous species as well as future related research on hydraulic implications after wounding.

Impact of a cost constraint on nutritionally adequate food choices for French women: an analysis by linear programming.

Science.gov (United States)

Darmon, Nicole; Ferguson, Elaine L; Briend, André

2006-01-01

To predict, for French women, the impact of a cost constraint on the food choices required to provide a nutritionally adequate diet. Isocaloric daily diets fulfilling both palatability and nutritional constraints were modeled in linear programming, using different cost constraint levels. For each modeled diet, total departure from an observed French population's average food group pattern ("mean observed diet") was minimized. To achieve the nutritional recommendations without a cost constraint, the modeled diet provided more energy from fish, fresh fruits and green vegetables and less energy from animal fats and cheese than the "mean observed diet." Introducing and strengthening a cost constraint decreased the energy provided by meat, fresh vegetables, fresh fruits, vegetable fat, and yogurts and increased the energy from processed meat, eggs, offal, and milk. For the lowest cost diet (ie, 3.18 euros/d), marked changes from the "mean observed diet" were required, including a marked reduction in the amount of energy from fresh fruits (-85%) and green vegetables (-70%), and an increase in the amount of energy from nuts, dried fruits, roots, legumes, and fruit juices. Nutrition education for low-income French women must emphasize these affordable food choices.

Hard- and software of real time simulation tools of Electric Power System for adequate modeling power semiconductors in voltage source convertor based HVDC and FACTS

Directory of Open Access Journals (Sweden)

Ufa Ruslan A.

2014-01-01

Full Text Available The motivation of the presented research is based on the needs for development of new methods and tools for adequate simulation of Flexible Alternating Current Transmission System (FACTS devices and High Voltage Direct Current Transmission (HVDC system as part of real electric power systems (EPS. For that, a hybrid approach for advanced simulation of the FACTS and HVDC based on Voltage Source is proposed. The presented simulation results of the developed hybrid model of VSC confirm the achievement of the desired properties of the model and the effectiveness of the proposed solutions.

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

Science.gov (United States)

Mahlab, Shelly; Linial, Michal

2014-01-01

Protein translation is the most expensive operation in dividing cells from bacteria to humans. Therefore, managing the speed and allocation of resources is subject to tight control. From bacteria to humans, clusters of relatively rare tRNA codons at the N′-terminal of mRNAs have been implicated in attenuating the process of ribosome allocation, and consequently the translation rate in a broad range of organisms. The current interpretation of “slow” tRNA codons does not distinguish between protein translations mediated by free- or endoplasmic reticulum (ER)-bound ribosomes. We demonstrate that proteins translated by free- or ER-bound ribosomes exhibit different overall properties in terms of their translation efficiency and speed in yeast, fly, plant, worm, bovine and human. We note that only secreted or membranous proteins with a Signal peptide (SP) are specified by segments of “slow” tRNA at the N′-terminal, followed by abundant codons that are considered “fast.” Such profiles apply to 3100 proteins of the human proteome that are composed of secreted and signal peptide (SP)-assisted membranous proteins. Remarkably, the bulks of the proteins (12,000), or membranous proteins lacking SP (3400), do not have such a pattern. Alternation of “fast” and “slow” codons was found also in proteins that translocate to mitochondria through transit peptides (TP). The differential clusters of tRNA adapted codons is not restricted to the N′-terminal of transcripts. Specifically, Glycosylphosphatidylinositol (GPI)-anchored proteins are unified by clusters of low adapted tRNAs codons at the C′-termini. Furthermore, selection of amino acids types and specific codons was shown as the driving force which establishes the translation demands for the secretory proteome. We postulate that “hard-coded” signals within the secretory proteome assist the steps of protein maturation and folding. Specifically, “speed control” signals for delaying the translation

The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea: high genome plasticity at intra-genus level

Directory of Open Access Journals (Sweden)

Pesole Graziano

2007-08-01

Full Text Available Abstract Background Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets are characterized by a remarkable stability of the mitochondrial (mt genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae. The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location. Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation

In vitro base modification of Escherichia coli glutamate 2 transfer-RNA and phenylalanine transfer-RNA gene transcripts

International Nuclear Information System (INIS)

Shahan, M.N.

1989-01-01

Plasmids were constructed that contain an E. Coli tRNA 2 Glu or tRNA Phe gene in a system transcribable by T7 or SP6 RNA polymerase. Selectively 32 P-labeled transcripts of these plasmids were used to study tRNA base modification in vitro in crude extracts by nearest neighbor analysis. The synthesis of 5-methyl-aminomethyl-2-thiouridine (mnm 5 s 2 U) was studied. Complete synthesis of mnm 5 s 2 2U is not observed. Instead, 2-thiouridine (s 2 U) is synthesized. Synthesis requires ATP, cysteine, Mg + , and monovalent cation concentrations below 50 mM. The reaction has a pH optimum above 7.0. Sulfide ion will substitute for cysteine in the reaction but sulfate, sulfite, methionine, homocysteine, and β-mercaptopyruvate will not. Extracts from E. coli strains carrying either the asuE or asuF mutations have reduced s 2 U synthetic activity which supports in vivo evidence that the wild type genes are involved in 2-thiolation of uridine. The enzyme is shown to be unstable both upon storage at -80 degree C and during the modification reaction. A method was developed to study the synthesis of any one of four pseudouridines ψ found at different positions of the tRNA cloverleaf. Synthesis of ψ is observed at three of the four positions-positions 32, 39, and 55. The asuC mutation is shown to affect ψ synthesis only at position 39 confirming that it is an allele of hisT and that the hisT mutations do not affect ψ synthesis at position 32 in E. coli. Synthesis of ψ32, ψ39, and ψ55 does not require any prior modification. Synthesis of dihydrouridine, 7-methylguanosine, and 3(3-amino-3-carboxypropyl)uridine is also observed. Synthesis of 2-methyladenosine and ψ 13 is not seen. Removal of part of the aminoacyl stem reduces synthesis of all modifications examined by 3' fold or more

Adequacy of a hospital-wide standard dose of 7mg/kg bodyweight gentamicin sufficient to achieve an adequate prophylactic maximum serum concentration (Cmax) in burn patients undergoing surgical burn wound treatment

NARCIS (Netherlands)

Borra, L.C.P.; Bosch, T.M.; Baar, M.E. van; Dokter, J.; Oen, I.M.; Ruijgrok, E.J.

2016-01-01

INTRODUCTION: Pharmacokinetics of drugs can be significantly altered in burn patients. The aim of our study was to validate if the current hospital-wide standard dosage of 7mg/kg total bodyweight gentamicin is sufficient to achieve an adequate prophylactic Cmax (Cmax>/=20mg/L). MATERIALS AND

[Functional restoration--it depends on an adequate mixture of treatment].

Science.gov (United States)

Pfingsten, M

2001-12-01

impairment as well as physical variables (mobility, strength) have limited predictive value. Return to work and pain reduction are much better predicted by length of absence from work, application for pension, and the patients' disability in daily-life activities. In the last five years another important variable of success has been identified: avoidance behavior has been suspected to be a major contributor to the initiation and maintenance of chronic low back pain. The perpetuation of avoidance behavior beyond normal healing time subsequently leads to negative consequences such as "disuse syndrome", which is associated with physical deconditioning, sick role behavior, psychosocial withdrawal and negative affect. Accordingly, fear-avoidance beliefs were strongly related to absenteeism from work due to back pain and were the best predictors of therapy outcome in 300 acute low back pain patients. In a prospective study on 87 patients with chronic low back pain (CLBP) we demonstrated that fear-avoidance beliefs were the strongest predictors of return to work after a functional restoration treatment program. Although nonspecific mechanisms such as emotional disturbance, helplessness, pain anticipation, disability, and job circumstances could be identified as influencing the chronic pain process, we have to remember that long-lasting experience of pain is usually a very individual process in which several conditions may work together in a unique combination. Treatment procedures must consider this variability by focusing on general mechanisms, as well as on individual conditions and deficits. FR treatment strongly depends on behavioral principles that rule the whole therapeutic process: Adequate information is necessary to overcome unhelpful beliefs; information has to be related to the patients' daily experiences and their mental capability to understand them. Pacing, goal-setting, graded exposure with exercise quotas and permanent feedback as well as contingent motivation

Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading

DEFF Research Database (Denmark)

Sørensen, Michael Askvad; Elf, J.; Bouakaz, E.

2005-01-01

During mRNA translation, synonymous codons for one amino acid are often read by different isoaccepting tRNAs. The theory of selective tRNA charging predicts greatly varying percentages of aminoacylation among isoacceptors in cells starved for their common amino acid. It also predicts major changes...... in tRNA charging patterns upon concentration changes of single isoacceptors, which suggests a novel type of translational control of gene expression. We therefore tested the theory by measuring with Northern blots the charging of Leu-tRNAs in Escherichia coli under Leu limitation in response to over...... postulated a previously unknown common codon for tRNALeu GAG and tRNALeu UAG. Subsequently, we demonstrated that the tRNALeu GAG codon CUU is, in fact, read also by tRNALeu UAG, due to a uridine-5-oxyacetic acid modification....

Is the world supply of omega-3 fatty acids adequate for optimal human nutrition?

Science.gov (United States)

Salem, Norman; Eggersdorfer, Manfred

2015-03-01

To delineate the available sources of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) for human consumption and to determine if the available supply is capable of supplying the nutrient levels recommended by expert bodies. There are converging opinions among experts, professional organizations and health professionals that a recommendation for a daily individual consumption of 500 mg of EPA/DHA would provide health benefits, and this translates to an annual human consumption of 1.3 million metric tons. Current human consumption of EPA/DHA is estimated to be only a small fraction of this amount and many people may suffer from suboptimal health as a result of low intake. EPA and DHA originate in the phytoplankton and are made available in the human food chain mainly through fish and other seafood. The fish catch is not elastic and in fact has long since reached a plateau. Aquaculture has grown rapidly, but most of the fish oil produced is currently being used to support aquaculture feed and so this would appear to limit aquaculture growth - or at least the growth in availability of fish sources of EPA/DHA. Vegetable oil-derived alpha-linolenic acid, though relatively plentiful, is converted only at a trace level in humans to DHA and not very efficiently to EPA, and so cannot fill this gap. Microbial EPA/DHA production can in the future be increased, although this oil is likely to remain more expensive than fish oil. Plant sources of EPA and DHA have now been produced in the laboratory via transgenic means and will eventually clear regulatory hurdles for commercialization, but societal acceptance remains in question. The purpose of this review is to discuss the various sources of omega-3 fatty acids within the context of the potential world demand for these nutrients. In summary, it is concluded that fish and vegetable oil sources will not be adequate to meet future needs, but that algal oil and terrestrial plants modified genetically to produce EPA and DHA

Selenoproteins in human body: focus on thyroid pathophysiology.

Science.gov (United States)

Valea, Ana; Georgescu, Carmen Emanuela

2018-06-05

Selenium (Se) has a multilevel, complex and dynamic effect on the human body as a major component of selenocysteine, incorporated into selenoproteins, which include the selenocysteine-containing enzymes iodothyronine deiodinases. At the thyroid level, these proteins play an essential role in antioxidant protection and hormone metabolism. This is a narrative review based on PubMed/Medline database research regarding thyroid physiology and conditions with Se and Se-protein interferences. In humans, Se-dependent enzyme functions are best expressed through optimal Se intake, although there is gap in our knowledge concerning the precise mechanisms underlying the interrelation. There is a good level of evidence linking low serum Se to autoimmune thyroid diseases and, to a lesser extent, differentiated thyroid cancer. However, when it comes to routine supplementation, the results are heterogeneous, except in the case of mild Graves' orbitopathy. Autoimmune hypothyroidism is associated with a state of higher oxidative stress, but not all studies found an improvement of thyroid function after Se was introduced as antioxidant support. Meanwhile, no routine supplementation is recommended. Low Se intake is correlated with an increased risk of developing antithyroid antibodies, its supplementation decreasing their titres; there is also a potential reduction in levothyroxine replacement dose required for hypothyroidism and/or the possibility that it prevents progression of subclinical hypothyroidism, although not all studies agree. In thyroid-associated orbitopathy, euthyroidism is more rapidly achieved if the micronutrient is added to traditional drugs, while controls appear to benefit from the microelement only if they are deficient; thus, a basal assay of Se appears advisable to better select patients who need substitution. Clearly, further Se status biomarkers are required. Future introduction of individual supplementation algorithms based on baseline micronutrient levels

Involving regional expertise in nationwide modeling for adequate prediction of climate change effects on different demands for fresh water

Science.gov (United States)

de Lange, W. J.

2014-05-01

Wim J. de Lange, Geert F. Prinsen, Jacco H. Hoogewoud, Ab A Veldhuizen, Joachim Hunink, Erik F.W. Ruijgh, Timo Kroon Nationwide modeling aims to produce a balanced distribution of climate change effects (e.g. harm on crops) and possible compensation (e.g. volume fresh water) based on consistent calculation. The present work is based on the Netherlands Hydrological Instrument (NHI, www.nhi.nu), which is a national, integrated, hydrological model that simulates distribution, flow and storage of all water in the surface water and groundwater systems. The instrument is developed to assess the impact on water use on land-surface (sprinkling crops, drinking water) and in surface water (navigation, cooling). The regional expertise involved in the development of NHI come from all parties involved in the use, production and management of water, such as waterboards, drinking water supply companies, provinces, ngo's, and so on. Adequate prediction implies that the model computes changes in the order of magnitude that is relevant to the effects. In scenarios related to drought, adequate prediction applies to the water demand and the hydrological effects during average, dry, very dry and extremely dry periods. The NHI acts as a part of the so-called Deltamodel (www.deltamodel.nl), which aims to predict effects and compensating measures of climate change both on safety against flooding and on water shortage during drought. To assess the effects, a limited number of well-defined scenarios is used within the Deltamodel. The effects on demand of fresh water consist of an increase of the demand e.g. for surface water level control to prevent dike burst, for flushing salt in ditches, for sprinkling of crops, for preserving wet nature and so on. Many of the effects are dealt with by regional and local parties. Therefore, these parties have large interest in the outcome of the scenario analyses. They are participating in the assessment of the NHI previous to the start of the analyses

Complete nucleotide sequence and gene rearrangement of the ...

Indian Academy of Sciences (India)

3Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China ... of these rearrangements involve tRNA genes, ND5 gene and ... ncbi.nlm.nih.gov/projects/Sequin/download/seq_win_download.

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.

[Neonatal ABO incompatibility underlies a potentially severe hemolytic disease of the newborn and requires adequate care].

Science.gov (United States)

Senterre, T; Minon, J-M; Rigo, J

2011-03-01

ABO allo-immunization is the most frequent hemolytic disease of the newborn and ABO incompatibility is present in 15-25 % of pregnancies. True ABO alloimmunization occurs in approximately one out of 150 births. Intensity is generally lower than in RhD allo-immunization. We report on three cases showing that ABO allo-immunization can lead to severe hemolytic disease of the newborn with potentially threatening hyperbilirubinemia and complications. Early diagnosis and adequate care are necessary to prevent complications in ABO incompatibility. A direct antiglobulin test is the cornerstone of diagnosis and should be performed at birth on cord blood sampling in all group infants born to O mothers, especially if of African origin. Risk factor analysis and attentive clinical monitoring during the first days of life are essential. Vigilance is even more important for infants discharged before the age of 72 h. Every newborn should be assessed for the risk of developing severe hyperbilirubinemia and should be examined by a qualified healthcare professional in the first days of life. Treatment depends on the total serum bilirubin level, which may increase very rapidly in the first 48 h of life in cases of hemolytic disease of the newborn. Phototherapy and, in severe cases, exchange transfusion are used to prevent hyperbilirubinemia encephalopathy. Intravenous immunoglobulins are used to reduce exchange transfusion. Treatments of severe hemolytic disease of the newborn should be provided and performed by trained personnel in neonatal intensive care units. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Do clinicians receive adequate training to identify trafficked persons? A scoping review of NHS Foundation Trusts.

Science.gov (United States)

Thompson, Charles Dr; Mahay, Arun; Stuckler, David; Steele, Sarah

2017-09-01

We investigate whether physicians in secondary care in the English NHS receive adequate training to recognise and appropriately refer for services those persons suspected to be victims of human trafficking. Freedom of Information requests were sent to the 105 England's NHS Trusts delivering acute care in England. NHS Trusts providing secondary care in England. English NHS Trusts. We requested data about the training provided on human trafficking to clinicians, including the nature, delivery, and format of any education, and any planned training. A total of 89.5% of the 105 Trusts responded. Of these Trusts, 69% provide education to physicians on human trafficking, and a further 6% provide training but did not specify who received it. The majority of Trusts providing training did so within wider safeguarding provision (91%). Only one trust reported that it provides stand-alone training on trafficking to all its staff, including physicians. Within training offered by Trusts, 54% observed best practice providing training on the clinical indicators of trafficking, while 16% referenced the National Referral Mechanism. Amongst those not providing training, 39% of Trusts report provision is in development. Our results find that 25% of NHS Foundation Trusts appear to lack training for physicians around human trafficking. It is also of concern that of the Trusts who currently do not provide training, only 39% are developing training or planning to do so. There is an urgent need to review and update the scope of available training and bring it into alignment with current legislation.

Perioperative antibiotics for surgical site infection in pancreaticoduodenectomy: does the SCIP-approved regimen provide adequate coverage?

Science.gov (United States)

Donald, Graham W; Sunjaya, Dharma; Lu, Xuyang; Chen, Formosa; Clerkin, Barbara; Eibl, Guido; Li, Gang; Tomlinson, James S; Donahue, Timothy R; Reber, Howard A; Hines, Oscar J

2013-08-01

The Joint Commission Surgical Care Improvement Project (SCIP) includes performance measures aimed at reducing surgical site infections (SSI). One measure defines approved perioperative antibiotics for general operative procedures. However, there may be a subset of procedures not adequately covered with the use of approved antibiotics. We hypothesized that piperacillin-tazobactam is a more appropriate perioperative antibiotic for pancreaticoduodenectomy (PD). In collaboration with hospital epidemiology and the Division of Infectious Diseases, we retrospectively reviewed records of 34 patients undergoing PD between March and May 2008 who received SCIP-approved perioperative antibiotics and calculated the SSI rate. After changing our perioperative antibiotic to piperacillin-tazobactam, we prospectively reviewed PDs performed between June 2008 and March 2009 and compared the SSI rates before and after the change. For 34 patients from March through May 2008, the SSI rate for PD was 32.4 per 100 cases. Common organisms from wound cultures were Enterobacter and Enterococcus (50.0% and 41.7%, respectively), and these were cefoxitin resistant. From June 2008 through March 2009, 106 PDs were performed. During this period, the SSI rate was 6.6 per 100 surgeries, 80% lower than during March through May 2008 (relative risk, 0.204; 95% confidence interval [CI], 0.086-0.485; P = .0004). Use of piperacillin-tazobactam as a perioperative antibiotic in PD may reduce SSI compared with the use of SCIP-approved antibiotics. Continued evaluation of SCIP performance measures in relationship to patient outcomes is integral to sustained quality improvement. Copyright © 2013 Mosby, Inc. All rights reserved.

Do clinicians receive adequate training to identify trafficked persons? A scoping review of NHS Foundation Trusts

Science.gov (United States)

Mahay, Arun; Stuckler, David; Steele, Sarah

2017-01-01

Objective We investigate whether physicians in secondary care in the English NHS receive adequate training to recognise and appropriately refer for services those persons suspected to be victims of human trafficking. Design Freedom of Information requests were sent to the 105 England’s NHS Trusts delivering acute care in England. Setting NHS Trusts providing secondary care in England. Participants English NHS Trusts. Main outcome measures We requested data about the training provided on human trafficking to clinicians, including the nature, delivery, and format of any education, and any planned training. Results A total of 89.5% of the 105 Trusts responded. Of these Trusts, 69% provide education to physicians on human trafficking, and a further 6% provide training but did not specify who received it. The majority of Trusts providing training did so within wider safeguarding provision (91%). Only one trust reported that it provides stand-alone training on trafficking to all its staff, including physicians. Within training offered by Trusts, 54% observed best practice providing training on the clinical indicators of trafficking, while 16% referenced the National Referral Mechanism. Amongst those not providing training, 39% of Trusts report provision is in development. Conclusions Our results find that 25% of NHS Foundation Trusts appear to lack training for physicians around human trafficking. It is also of concern that of the Trusts who currently do not provide training, only 39% are developing training or planning to do so. There is an urgent need to review and update the scope of available training and bring it into alignment with current legislation. PMID:28904806

Different behaviour of 63Ni and 59Fe during absorption in iron-deficient and iron-adequate jejunal rat segments ex vivo

International Nuclear Information System (INIS)

Mueller-Fassbender, M.; Elsenhans, B.; McKie, A.T.; Schuemann, K.

2003-01-01

Nickel exhibits low oral toxicity. It shares the absorptive pathways for iron, though there are substantial quantitative differences in handling of both metals. To analyse these differences more closely, jejunal segments from iron-deficient and iron-adequate rats were luminally perfused ex vivo with 59 Fe and 63 Ni at six different concentrations (1-500 μmo1/l) under steady state conditions. 59 Fe over-all absorption increased 2.0-4.6-fold in iron-deficiency at luminal concentrations between 1 and 100 μmol/l, while 63 Ni absorption increased to a much lower extent (2.6-fold at 1 μmol/l and 1.5-fold at higher luminal concentrations). Moreover, there was a 5-7-fold higher concentration for 63 Ni in the jejunal tissue than in the absorbate at luminal concentrations above 50 μmol/l which was not observed at 1 μmol 63 Ni/l and not for 59 Fe. 63 Ni tissue load showed a linear and a saturable fraction. In iron-deficiency the saturable 63 Ni fraction increased 4-fold as compared to only 1.5-fold increments for 59 Fe. Moreover, a substantially higher share of 63 Ni was retained in the jejunal tissue at high as compare to low luminal concentrations after perfusion had been continued without luminal radioactivity. This was not found for 59 Fe and suggests a concentration-dependent block of 63 Ni export across the enterocytes' basolateral membrane. To explain these results one may speculate that 63 Ni may bind more tightly to tissue ligands than 59 Fe due to the higher thermodynamic and kinetic stability of nickel complexes. In particular, nickel may bind to a basolateral population of metal carriers and block its own basolateral transfer in a concentration-dependent manner. Tight 63 Ni binding to non-specific jejunal ligands is responsible for the unaltered high linear fraction of jejunal 63 Ni load in iron-deficient and iron-adequate segments. Binding of 63 Ni to food and tissue ligands in the small intestine may, thus, be a likely explanation for the low oral nickel

Are parents in the UK equipped to provide adequate burns first aid?

Science.gov (United States)

Graham, Hamish E; Bache, Sarah E; Muthayya, Preetha; Baker, Julie; Ralston, David R

2012-05-01

Simple first aid following a burn injury has been shown to improve outcome. With this in mind, a prospective study was conducted to evaluate the knowledge of burns first aid amongst parents in South Yorkshire, United Kingdom. This information was used to identify which aspects of burn first aid need to be highlighted in an education campaign and who the target audience should be. A simple mnemonic is suggested to assist parental education on the topic. Parents attending outpatient clinics at Sheffield Children's Hospital were interviewed and asked about the first aid they would provide for a child with a large scald. Removal of hot clothes and jewellery; application of cold water for 10-20 min; obtaining medical advice; and covering the burn with a plastic film or clean cloth were all considered to be ideal responses. Variations in responses in relation to the age and ethnicity of the parent were noted. One hundred and eighty eight parents were included in the questionnaire. Of these, 81% (n=152) were white British and 20% (n=36) were from other ethnic groups. Only 10% (n=18) of all respondent would give all the ideal first aid steps. Less than 40% (n=73) of parents questioned would remove hot clothes and jewellery. There was no significant difference in responses between ethnic groups when assessing knowledge of the need to remove hot soaked clothing. Although 73% (n=137) of parents would run the burn under cool water, only 35% (n=66) would cool the burn for an adequate length of time. White British parents were significantly more likely to run cool water over the burn, and to continue this for the recommended 10-20 min. Whilst 88% (n=165) of parents would seek medical attention, this was significantly less in parents under 20 years old. Finally, 92% (n=173) of parents would protect the wound with appropriate dressings, but of note, 26% (n=9) of parents from minority ethnic groups would potentially impair burn healing by using inappropriate dressings and topical