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Sample records for ribosomal exit tunnel

  1. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel

    DEFF Research Database (Denmark)

    Wekselman, Itai; Zimmerman, Ella; Davidovich, Chen

    2017-01-01

    Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal...... of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within...

  2. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel

    Energy Technology Data Exchange (ETDEWEB)

    Metelev, Mikhail; Osterman, Ilya A.; Ghilarov, Dmitry; Khabibullina, Nelli F.; Yakimov, Alexander; Shabalin, Konstantin; Utkina, Irina; Travin, Dmitry Y.; Komarova, Ekaterina S.; Serebryakova, Marina; Artamonova, Tatyana; Khodorkovskii, Mikhail; Konevega, Andrey L.; Sergiev, Petr V.; Severinov, Konstantin; Polikanov, Yury S.

    2017-08-28

    Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome–KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.

  3. A conserved chloramphenicol binding site at the entrance to the ribosomal peptide exit tunnel

    DEFF Research Database (Denmark)

    Long, Katherine S; Porse, Bo T

    2003-01-01

    , of E.coli 23S rRNA and G2084 (2058 in E.coli numbering) in domain V of H.halobium 23S rRNA. The modification sites overlap with a portion of the macrolide binding site and cluster at the entrance to the peptide exit tunnel. The data correlate with the recently reported chloramphenicol binding site...... on an archaeal ribosome and suggest that a similar binding site is present on the E.coli ribosome....

  4. The ribosomal protein uL22 modulates the shape of the nascent protein exit tunnel

    DEFF Research Database (Denmark)

    Wekselman, I.; Zimmerman, E.; Davidovich, C.

    2017-01-01

    in the entrance of theribosomal exit tunnel and interferes with the progression of nas-cent chains. Commonly, resistance to erythromycin is acquiredby alterations of rRNA nucleotides that interact with the drug.Mutations in theb-hairpin of ribosomal protein uL22, which israther distal to the erythromycin binding...... to erythromycin binding pocket and increases its flexi-bility. Based on our results, we suggest a feasble mechanism thatexplains how nanscent proteins can be translated when ery-thromycin is bound to the ribosome. Furthermore, our findingssupport recent studies showing that the interactions betweenuL22...

  5. Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.

    Science.gov (United States)

    Greber, Basil Johannes; Gerhardy, Stefan; Leitner, Alexander; Leibundgut, Marc; Salem, Michèle; Boehringer, Daniel; Leulliot, Nicolas; Aebersold, Ruedi; Panse, Vikram Govind; Ban, Nenad

    2016-01-14

    Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. An exit cavity was crucial to the polymerase activity of the early ribosome.

    Science.gov (United States)

    Fox, George E; Tran, Quyen; Yonath, Ada

    2012-01-01

    The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptide bond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di- or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World.

  7. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

    International Nuclear Information System (INIS)

    Kurkcuoglu, Ozge; Doruker, Pemra; Jernigan, Robert L; Sen, Taner Z; Kloczkowski, Andrzej

    2008-01-01

    The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine–Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit

  8. Tunneling time, exit time and exit momentum in strong field tunnel ionization

    International Nuclear Information System (INIS)

    Teeny, Nicolas

    2016-01-01

    Tunnel ionization belongs to the fundamental processes of atomic physics. It is still an open question when does the electron tunnel ionize and how long is the duration of tunneling. In this work we solve the time-dependent Schroedinger equation in one and two dimensions and use ab initio quantum calculations in order to answer these questions. Additionally, we determine the exit momentum of the tunnel ionized electron from first principles. We find out results that are different from the assumptions of the commonly employed two-step model, which assumes that the electron ionizes at the instant of electric field maximum with a zero momentum. After determining the quantum final momentum distribution of tunnel ionized electrons we show that the two-step model fails to predict the correct final momentum. Accordingly we suggest how to correct the two-step model. Furthermore, we determine the instant at which tunnel ionization starts, which turns out to be different from the instant usually assumed. From determining the instant at which it is most probable for the electron to enter the tunneling barrier and the instant at which it exits we determine the most probable time spent under the barrier. Moreover, we apply a quantum clock approach in order to determine the duration of tunnel ionization. From the quantum clock we determine an average tunneling time which is different in magnitude and origin with respect to the most probable tunneling time. By defining a probability distribution of tunneling times using virtual detectors we relate both methods and explain the apparent discrepancy. The results found have in general an effect on the interpretation of experiments that measure the spectra of tunnel ionized electrons, and specifically on the calibration of the so called attoclock experiments, because models with imprecise assumptions are usually employed in order to interpret experimental results.

  9. Tunneling time, exit time and exit momentum in strong field tunnel ionization

    Energy Technology Data Exchange (ETDEWEB)

    Teeny, Nicolas

    2016-10-18

    Tunnel ionization belongs to the fundamental processes of atomic physics. It is still an open question when does the electron tunnel ionize and how long is the duration of tunneling. In this work we solve the time-dependent Schroedinger equation in one and two dimensions and use ab initio quantum calculations in order to answer these questions. Additionally, we determine the exit momentum of the tunnel ionized electron from first principles. We find out results that are different from the assumptions of the commonly employed two-step model, which assumes that the electron ionizes at the instant of electric field maximum with a zero momentum. After determining the quantum final momentum distribution of tunnel ionized electrons we show that the two-step model fails to predict the correct final momentum. Accordingly we suggest how to correct the two-step model. Furthermore, we determine the instant at which tunnel ionization starts, which turns out to be different from the instant usually assumed. From determining the instant at which it is most probable for the electron to enter the tunneling barrier and the instant at which it exits we determine the most probable time spent under the barrier. Moreover, we apply a quantum clock approach in order to determine the duration of tunnel ionization. From the quantum clock we determine an average tunneling time which is different in magnitude and origin with respect to the most probable tunneling time. By defining a probability distribution of tunneling times using virtual detectors we relate both methods and explain the apparent discrepancy. The results found have in general an effect on the interpretation of experiments that measure the spectra of tunnel ionized electrons, and specifically on the calibration of the so called attoclock experiments, because models with imprecise assumptions are usually employed in order to interpret experimental results.

  10. Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing.

    Science.gov (United States)

    Gamalinda, Michael; Jakovljevic, Jelena; Babiano, Reyes; Talkish, Jason; de la Cruz, Jesús; Woolford, John L

    2013-02-01

    Ribosome synthesis involves the coordinated folding and processing of pre-rRNAs with assembly of ribosomal proteins. In eukaryotes, these events are facilitated by trans-acting factors that propel ribosome maturation from the nucleolus to the cytoplasm. However, there is a gap in understanding how ribosomal proteins configure pre-ribosomes in vivo to enable processing to occur. Here, we have examined the role of adjacent yeast r-proteins L17, L35 and L37 in folding and processing of pre-rRNAs, and binding of other proteins within assembling ribosomes. These three essential ribosomal proteins, which surround the polypeptide exit tunnel, are required for 60S subunit formation as a consequence of their role in removal of the ITS2 spacer from 27SB pre-rRNA. L17-, L35- and L37-depleted cells exhibit turnover of aberrant pre-60S assembly intermediates. Although the structure of ITS2 does not appear to be grossly affected in their absence, these three ribosomal proteins are necessary for efficient recruitment of factors required for 27SB pre-rRNA processing, namely, Nsa2 and Nog2, which associate with pre-60S ribosomal particles containing 27SB pre-rRNAs. Altogether, these data support that L17, L35 and L37 are specifically required for a recruiting step immediately preceding removal of ITS2.

  11. Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain.

    Science.gov (United States)

    Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan; Polacek, Norbert

    2017-06-20

    The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson-Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Dual binding mode of the nascent polypeptide-associated complex reveals a novel universal adapter site on the ribosome.

    Science.gov (United States)

    Pech, Markus; Spreter, Thomas; Beckmann, Roland; Beatrix, Birgitta

    2010-06-18

    Nascent polypeptide-associated complex (NAC) was identified in eukaryotes as the first cytosolic factor that contacts the nascent polypeptide chain emerging from the ribosome. NAC is present as a homodimer in archaea and as a highly conserved heterodimer in eukaryotes. Mutations in NAC cause severe embryonically lethal phenotypes in mice, Drosophila melanogaster, and Caenorhabditis elegans. In the yeast Saccharomyces cerevisiae NAC is quantitatively associated with ribosomes. Here we show that NAC contacts several ribosomal proteins. The N terminus of betaNAC, however, specifically contacts near the tunnel exit ribosomal protein Rpl31, which is unique to eukaryotes and archaea. Moreover, the first 23 amino acids of betaNAC are sufficient to direct an otherwise non-associated protein to the ribosome. In contrast, alphaNAC (Egd2p) contacts Rpl17, the direct neighbor of Rpl31 at the ribosomal tunnel exit site. Rpl31 was also recently identified as a contact site for the SRP receptor and the ribosome-associated complex. Furthermore, in Escherichia coli peptide deformylase (PDF) interacts with the corresponding surface area on the eubacterial ribosome. In addition to the previously identified universal adapter site represented by Rpl25/Rpl35, we therefore refer to Rpl31/Rpl17 as a novel universal docking site for ribosome-associated factors on the eukaryotic ribosome.

  13. Background noise measurements from jet exit vanes designed to reduced flow pulsations in an open-jet wind tunnel

    Science.gov (United States)

    Hoad, D. R.; Martin, R. M.

    1985-01-01

    Many open jet wind tunnels experience pulsations of the flow which are typically characterized by periodic low frequency velocity and pressure variations. One method of reducing these fluctuations is to install vanes around the perimeter of the jet exit to protrude into the flow. Although these vanes were shown to be effective in reducing the fluctuation content, they can also increase the test section background noise level. The results of an experimental acoustic program in the Langley 4- by 7-Meter Tunnel is presented which evaluates the effect on tunnel background noise of such modifications to the jet exit nozzle. Noise levels for the baseline tunnel configuration are compared with those for three jet exit nozzle modifications, including an enhanced noise reduction configuration that minimizes the effect of the vanes on the background noise. Although the noise levels for this modified vane configuration were comparable to baseline tunnel background noise levels in this facility, installation of these modified vanes in an acoustic tunnel may be of concern because the noise levels for the vanes could be well above background noise levels in a quiet facility.

  14. Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.

    Science.gov (United States)

    Sandikci, Arzu; Gloge, Felix; Martinez, Michael; Mayer, Matthias P; Wade, Rebecca; Bukau, Bernd; Kramer, Günter

    2013-07-01

    Newly synthesized polypeptides undergo various cotranslational maturation steps, including N-terminal enzymatic processing, chaperone-assisted folding and membrane targeting, but the spatial and temporal coordination of these steps is unclear. We show that Escherichia coli methionine aminopeptidase (MAP) associates with ribosomes through a charged loop that is crucial for nascent-chain processing and cell viability. MAP competes with peptide deformylase (PDF), the first enzyme to act on nascent chains, for binding sites at the ribosomal tunnel exit. PDF has extremely fast association and dissociation kinetics, which allows it to frequently sample ribosomes and ensure the processing of nascent chains after their emergence. Premature recruitment of the chaperone trigger factor, or polypeptide folding, negatively affect processing efficiency. Thus, the fast ribosome association kinetics of PDF and MAP are crucial for the temporal separation of nascent-chain processing from later maturation events, including chaperone recruitment and folding.

  15. Reduction of exit-site infections of tunnelled intravascular catheters among neutropenic patients by sustained-release chlorhexidine dressings: results from a prospective randomized controlled trial.

    Science.gov (United States)

    Chambers, S T; Sanders, J; Patton, W N; Ganly, P; Birch, M; Crump, J A; Spearing, R L

    2005-09-01

    Exit-site and tunnel infections of tunnelled central intravascular catheters are a frequent source of morbidity among neutropenic patients and may necessitate catheter removal. They require antimicrobial therapy that increases healthcare costs and is associated with adverse drug reactions. A prospective randomized clinical trial was conducted among adult patients undergoing chemotherapy in a haematology unit. Tunnelled intravascular catheters were randomized to receive the control of a standard dressing regimen as recommended by the British Committee for Standards in Haematology, or to receive the intervention of a sustained-release chlorhexidine dressing. Follow-up data were available in 112 of 114 tunnelled intravascular catheters which were randomized. Exit-site or combined exit-site/tunnel infections occurred in 23 (43%) of 54 catheters in the control group, and five (9%) of 58 catheters in the intervention group [odds ratio (OR) for intervention group compared with control group =0.13, 95% confidence intervals (CI) 0.04-0.37, P<0.001]. More tunnelled intravascular catheters were prematurely removed from the control group than the intervention group for documented infections [20/54 (37%) vs 6/58 (10%), OR=0.20, 95%CI 0.53-0.07]. However, there was no difference in the numbers of tunnelled intravascular catheters removed for all proven and suspected intravascular catheter-related infections [21/54 (39%) vs 19/58 (33%)], or in the time to removal of catheters for any reason other than death or end of treatment for underlying disease. Thus chlorhexidine dressings reduced the incidence of exit-site/tunnel infections of indwelling tunnelled intravascular catheters without prolonging catheter survival in neutropenic patients, and could be considered as part of the routine management of indwelling tunnelled intravascular catheters among neutropenic patients.

  16. Reduction of background noise induced by wind tunnel jet exit vanes

    Science.gov (United States)

    Martin, R. M.; Brooks, T. F.; Hoad, D. R.

    1985-01-01

    The NASA-Langley 4 x 7 m wind tunnel develops low frequency flow pulsations at certain velocity ranges during open throat mode operation, affecting the aerodynamics of the flow and degrading the resulting model test data. Triangular vanes attached to the trailing edge of flat steel rails, mounted 10 cm from the inside of the jet exit walls, have been used to reduce this effect; attention is presently given to methods used to reduce the inherent noise generation of the vanes while retaining their pulsation reduction features.

  17. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome

    Science.gov (United States)

    Merz, Frieder; Boehringer, Daniel; Schaffitzel, Christiane; Preissler, Steffen; Hoffmann, Anja; Maier, Timm; Rutkowska, Anna; Lozza, Jasmin; Ban, Nenad; Bukau, Bernd; Deuerling, Elke

    2008-01-01

    Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome–nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors. PMID:18497744

  18. Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome.

    Science.gov (United States)

    Jomaa, Ahmad; Fu, Yu-Hsien Hwang; Boehringer, Daniel; Leibundgut, Marc; Shan, Shu-Ou; Ban, Nenad

    2017-05-19

    During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the 'activated' SRP-SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon.

  19. The complete structure of the large subunit of the mammalian mitochondrial ribosome.

    Science.gov (United States)

    Greber, Basil J; Boehringer, Daniel; Leibundgut, Marc; Bieri, Philipp; Leitner, Alexander; Schmitz, Nikolaus; Aebersold, Ruedi; Ban, Nenad

    2014-11-13

    Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.

  20. Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex.

    Science.gov (United States)

    Xie, Ping

    2015-10-09

    Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by "hungry" codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.

  1. Hybrid inflation exit through tunneling

    International Nuclear Information System (INIS)

    Garbrecht, Bjoern; Konstandin, Thomas

    2007-01-01

    For hybrid inflationary potentials, we derive the tunneling rate from field configurations along the flat direction towards the waterfall regime. This process competes with the classically rolling evolution of the scalar fields and needs to be strongly subdominant for phenomenologically viable models. Tunneling may exclude models with a mass scale below 10 12 GeV, but can be suppressed by small values of the coupling constants. We find that tunneling is negligible for those models, which do not require fine tuning in order to cancel radiative corrections, in particular for GUT-scale SUSY inflation. In contrast, electroweak scale hybrid inflation is not viable, unless the inflaton-waterfall field coupling is smaller than approximately 10 -11

  2. The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.

    Science.gov (United States)

    Bieri, Philipp; Leibundgut, Marc; Saurer, Martin; Boehringer, Daniel; Ban, Nenad

    2017-02-15

    Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  3. Jet Exit Rig Six Component Force Balance

    Science.gov (United States)

    Castner, Raymond; Wolter, John; Woike, Mark; Booth, Dennis

    2012-01-01

    A new six axis air balance was delivered to the NASA Glenn Research Center. This air balance has an axial force capability of 800 pounds, primary airflow of 10 pounds per second, and a secondary airflow of 3 pounds per second. Its primary use was for the NASA Glenn Jet Exit Rig, a wind tunnel model used to test both low-speed, and high-speed nozzle concepts in a wind tunnel. This report outlines the installation of the balance in the Jet Exit Rig, and the results from an ASME calibration nozzle with an exit area of 8 square-inches. The results demonstrated the stability of the force balance for axial measurements and the repeatability of measurements better than 0.20 percent.

  4. Exit site and tunnel infections in children on chronic peritoneal dialysis: findings from the Standardizing Care to Improve Outcomes in Pediatric End Stage Renal Disease (SCOPE) Collaborative.

    Science.gov (United States)

    Swartz, Sarah J; Neu, Alicia; Skversky Mason, Amy; Richardson, Troy; Rodean, Jonathan; Lawlor, John; Warady, Bradley; Somers, Michael J G

    2018-06-01

    The Standardizing Care to Improve Outcomes in Pediatric End Stage Renal Disease (SCOPE) Collaborative is a quality improvement initiative to reduce dialysis-associated infections. The frequency of peritoneal dialysis (PD) catheter exit site infection (ESI) and variables influencing its development and end result are unclear. We sought to determine ESI rates, to elucidate the epidemiology, risk factors, and outcomes for ESI, and to assess for association between provider compliance with care bundles and ESI risk. We reviewed demographic, dialysis and ESI data, and care bundle adherence and outcomes for SCOPE enrollees from October 2011 to September 2014. ESI involved only the exit site, only the subcutaneous catheter tunnel, or both. A total of 857 catheter insertions occurred in 734 children over 10,110 cumulative months of PD provided to these children. During this period 207 ESIs arose in 124 children or 0.25 ESIs per dialysis year. Median time to ESI was 392 days, with 69% of ESIs involving exit site only, 23% involving the tunnel only, and 8% involving both sites. Peritonitis developed in 6%. ESI incidence was associated with age (p = 0.003), being the lowest in children aged  0 at prior month's visit (p treatment, 24% required hospitalization, and 9% required catheter removal, generally secondary to tunnel infection. Exit site infections occur at an annualized rate of 0.25, typically well into the dialysis course. Younger patient age and documented review of site care are associated with lower ESI rates. Although most ESIs resolve, hospitalization is frequent, and tunnel involvement/catheter loss complicate outcomes.

  5. Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin

    Directory of Open Access Journals (Sweden)

    Fucini Paola

    2004-04-01

    Full Text Available Abstract Background The bacterial ribosome is a primary target of several classes of antibiotics. Investigation of the structure of the ribosomal subunits in complex with different antibiotics can reveal the mode of inhibition of ribosomal protein synthesis. Analysis of the interactions between antibiotics and the ribosome permits investigation of the specific effect of modifications leading to antimicrobial resistances. Streptogramins are unique among the ribosome-targeting antibiotics because they consist of two components, streptogramins A and B, which act synergistically. Each compound alone exhibits a weak bacteriostatic activity, whereas the combination can act bactericidal. The streptogramins A display a prolonged activity that even persists after removal of the drug. However, the mode of activity of the streptogramins has not yet been fully elucidated, despite a plethora of biochemical and structural data. Results The investigation of the crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with the clinically relevant streptogramins quinupristin and dalfopristin reveals their unique inhibitory mechanism. Quinupristin, a streptogramin B compound, binds in the ribosomal exit tunnel in a similar manner and position as the macrolides, suggesting a similar inhibitory mechanism, namely blockage of the ribosomal tunnel. Dalfopristin, the corresponding streptogramin A compound, binds close to quinupristin directly within the peptidyl transferase centre affecting both A- and P-site occupation by tRNA molecules. Conclusions The crystal structure indicates that the synergistic effect derives from direct interaction between both compounds and shared contacts with a single nucleotide, A2062. Upon binding of the streptogramins, the peptidyl transferase centre undergoes a significant conformational transition, which leads to a stable, non-productive orientation of the universally conserved U2585. Mutations of this r

  6. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

    Science.gov (United States)

    Fritch, Benjamin; Kosolapov, Andrey; Hudson, Phillip; Nissley, Daniel A; Woodcock, H Lee; Deutsch, Carol; O'Brien, Edward P

    2018-04-18

    Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.

  7. The relationship of lateral anatomic structures to exiting guide pins during femoral tunnel preparation utilizing an accessory medial portal.

    Science.gov (United States)

    Farrow, Lutul D; Parker, Richard D

    2010-06-01

    Anatomic reconstruction of the anterior cruciate ligament through an accessory medial portal has become increasingly popular. The purpose of this study is to describe the relationship of guide pin exit points to the lateral anatomic structures when preparing the anterior cruciate ligament femoral tunnel through an accessory medial portal. We utilized seven fresh frozen cadaveric knees. Utilizing an anteromedial approach, a guide wire was placed into the center of each bundle's footprint. Each guide wire was advanced through the lateral femoral cortex. The guide pins were passed at 90, 110, and 130 degrees of knee flexion. The distances from each guide pin to the closest relevant structures on the lateral side of the knee were measured. At 90 degrees the posterolateral bundle guide pin was closest to the lateral condyle articular cartilage (mean 5.4 +/- 2.2 mm) and gastrocnemius tendon (mean 5.7 +/- 2.1 mm). At 110 degrees the posterolateral bundle pin was closest to the gastrocnemius tendon (mean 4.5 +/- 3.4 mm). At 130 degrees the posterolateral bundle pin was closest to the gastrocnemius tendon (mean 7.2 +/- 5.5 mm) and lateral collateral ligament (mean 6.8 +/- 2.1 mm). At 90 degrees the anteromedial bundle guide pin was closest to the articular cartilage (mean 2.0 +/- 2.0 mm). At 110 degrees the anteromedial bundle pin was closest to the articular cartilage (mean 7.4 +/- 3.5 mm) and gastrocnemius tendon (mean 12.3 +/- 3.1 mm). At 130 degrees the AM bundle pin was closest to the gastrocnemius tendon (mean 8.2 +/- 3.2 mm) and LCL (mean 15.1 +/- 2.9 mm). Neither guide pin (anteromedial or posterolateral bundle) put the peroneal nerve at risk at any knee flexion angle. At low knee flexion angles the anteromedial and posterolateral bundle guide pins closely approximated multiple lateral structures when using an accessory medial arthroscopic portal. Utilizing higher flexion angles increases the margin of error when preparing both femoral tunnels. During preparation of

  8. Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography.

    Science.gov (United States)

    Englmeier, Robert; Pfeffer, Stefan; Förster, Friedrich

    2017-10-03

    Mitochondria maintain their own genome and its corresponding protein synthesis machine, the mitochondrial ribosome (mitoribosome). Mitoribosomes primarily synthesize highly hydrophobic proteins of the inner mitochondrial membrane. Recent studies revealed the complete structure of the isolated mammalian mitoribosome, but its mode of membrane association remained hypothetical. In this study, we used cryoelectron tomography to visualize human mitoribosomes in isolated mitochondria. The subtomogram average of the membrane-associated human mitoribosome reveals a single major contact site with the inner membrane, mediated by the mitochondria-specific protein mL45. A second rRNA-mediated contact site that is present in yeast is absent in humans, resulting in a more variable association of the human mitoribosome with the inner membrane. Despite extensive structural differences of mammalian and fungal mitoribosomal structure, the principal organization of peptide exit tunnel and the mL45 homolog remains invariant, presumably to align the mitoribosome with the membrane-embedded insertion machinery. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Architecture of the large subunit of the mammalian mitochondrial ribosome.

    Science.gov (United States)

    Greber, Basil J; Boehringer, Daniel; Leitner, Alexander; Bieri, Philipp; Voigts-Hoffmann, Felix; Erzberger, Jan P; Leibundgut, Marc; Aebersold, Ruedi; Ban, Nenad

    2014-01-23

    Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.

  10. Investigation of air flow in open-throat wind tunnels

    Science.gov (United States)

    Jacobs, Eastman N

    1930-01-01

    Tests were conducted on the 6-inch wind tunnel of the National Advisory Committee for Aeronautics to form a part of a research on open-throat wind tunnels. The primary object of this part of the research was to study a type of air pulsation which has been encountered in open-throat tunnels, and to find the most satisfactory means of eliminating such pulsations. In order to do this it was necessary to study the effects of different variable on all of the important characteristics of the tunnel. This paper gives not only the results of the study of air pulsations and methods of eliminating them, but also the effects of changing the exit-cone diameter and flare and the effects of air leakage from the return passage. It was found that the air pulsations in the 6-inch wind tunnel could be practically eliminated by using a moderately large flare on the exit cone in conjunction with leakage introduced by cutting holes in the exit cone somewhat aft of its minimum diameter.

  11. The Dynamics of SecM-Induced Translational Stalling

    Directory of Open Access Journals (Sweden)

    Albert Tsai

    2014-06-01

    Full Text Available SecM is an E. coli secretion monitor capable of stalling translation on the prokaryotic ribosome without cofactors. Biochemical and structural studies have demonstrated that the SecM nascent chain interacts with the 50S subunit exit tunnel to inhibit peptide bond formation. However, the timescales and pathways of stalling on an mRNA remain undefined. To provide a dynamic mechanism for stalling, we directly tracked the dynamics of elongation on ribosomes translating the SecM stall sequence (FSTPVWISQAQGIRAGP using single-molecule fluorescence techniques. Within 1 min, three peptide-ribosome interactions work cooperatively over the last five codons of the SecM sequence, leading to severely impaired elongation rates beginning from the terminal proline and lasting four codons. Our results suggest that stalling is tightly linked to the dynamics of elongation and underscore the roles that the exit tunnel and nascent chain play in controlling fundamental steps in translation.

  12. THE ROLE OF ASTRO-GEODETIC IN PRECISE GUIDANCE OF LONG TUNNELS

    Directory of Open Access Journals (Sweden)

    M. Mirghasempour

    2015-12-01

    Full Text Available One of prime aspects of surveying projects is guidance of paths of a long tunnel from different directions and finally ending all paths in a specific place. This kind of underground surveying, because of particular condition, has some different points in relation to the ground surveying, including Improper geometry in underground transverse, low precise measurement in direction and length due to condition such as refraction, distinct gravity between underground point and corresponding point on the ground (both value and direction of gravity and etc. To solve this problems, astro-geodetic that is part of geodesy science, can help surveying engineers. In this article, the role of astronomy is defined in two subjects: 1- Azimuth determination of directions from entrance and exit nets of tunnel and also calibration of gyro-theodolite to use them in Underground transvers: By astronomical methods, azimuth of directions can be determine with an accuracy of 0.5 arcsecond, whereas, nowadays, no gyroscope can measure the azimuth in this accuracy; For instance, accuracy of the most precise gyroscope (Gyromat 5000 is 1.2 cm over a distance of one kilometre (2.4 arcsecond. Furthermore, the calibration methods that will be mention in this article, have significance effects on underground transverse. 2- Height relation between entrance point and exit point is problematic and time consuming; For example, in a 3 km long tunnel ( in Arak- Khoram Abad freeway, to relate entrance point to exit point, it is necessary to perform levelling about 90 km. Other example of this boring and time consuming levelling is in Kerman tunnel. This tunnel is 36 km length, but to transfer the entrance point height to exit point, 150 km levelling is needed. According to this paper, The solution for this difficulty is application of astro-geodetic and determination of vertical deflection by digital zenith camera system TZK2-D. These two elements make possible to define geoid profile

  13. Social influence in a virtual tunnel fire--influence of conflicting information on evacuation behavior.

    Science.gov (United States)

    Kinateder, Max; Müller, Mathias; Jost, Michael; Mühlberger, Andreas; Pauli, Paul

    2014-11-01

    Evacuation from a smoke filled tunnel requires quick decision-making and swift action from the tunnel occupants. Technical installations such as emergency signage aim to guide tunnel occupants to the closest emergency exits. However, conflicting information may come from the behavior of other tunnel occupants. We examined if and how conflicting social information may affect evacuation in terms of delayed and/or inadequate evacuation decisions and behaviors. To this end, forty participants were repeatedly situated in a virtual reality smoke filled tunnel with an emergency exit visible to one side of the participants. Four social influence conditions were realized. In the control condition participants were alone in the tunnel, while in the other three experimental conditions a virtual agent (VA) was present. In the no-conflict condition, the VA moved to the emergency exit. In the active conflict condition, the VA moved in the opposite direction of the emergency exit. In the passive conflict condition, the VA stayed passive. Participants were less likely to move to the emergency exit in the conflict conditions compared to the no-conflict condition. Pre-movement and movement times in the passive conflict condition were significantly delayed compared to all other conditions. Participants moved the longest distances in the passive conflict condition. These results support the hypothesis that social influence affects evacuation behavior, especially passive behavior of others can thwart an evacuation to safety. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  14. Insertion of a straight peritoneal catheter in an arcuate subcutaneous tunnel by a tunneler: long-term experience.

    Science.gov (United States)

    Favazza, A; Petri, R; Montanaro, D; Boscutti, G; Bresadola, F; Mioni, G

    1995-01-01

    This study describes the results of the insertion of a straight Tenckhoff peritoneal catheter (PC) in an arcuate, caudally concave tunnel using a tunneler designed by the authors. It has a semicircular shape and a bending radius of 4.5 cm. A hospital renal unit. From June 1988 to February 1994, 112 straight Tenckhoff PCs, 62 with one deep cuff (single-cuff PC) and 50 with two cuffs (double-cuff PC), were inserted as first catheters in 112 patients (mean age 62 +/- 13 years), who underwent continuous ambulatory peritoneal dialysis (CAPD). The follow-up was 1099 months (mean 18 +/- 13 months) for single-cuff PCs and 1264 months (mean 25 +/- 15 months) for double-cuff PCs, respectively. After intraperitoneal placement of the PCs by median laparotomy, a 180 degrees arc bend tunnel, with both external and peritoneal exits directed downwards, was created by means of the tunneler. The rate of exit-site infection (ESI) was 0.27 episodes/year (epis/year). The probability of remaining ESI-free was 76%, 60%, and 55% at 1, 2, and 3 years. The rate of tunnel infection (TI) was 0.046 epis/year. The incidence of the double-cuff PC-related ESI and TI tended to be lower than the incidence observed with the single-cuff PC. Episodes of peritonitis were 60 (0.30 epis/year), where 6 were subsequent to ESI and/or TI. Two PCs were lost due to ESI, 3 due to TI, and 11 due to peritonitis. Drainage failure, due to displacement of the PC caused by straightening, involved 3 PCs; 2 were lost. PC survival was 92%, 82%, and 74% at 1, 2 and 3 years, respectively. By an easily used semicircular tunneler, the standard straight Tenckhoff PC can be stably positioned in an arcuate tunnel with both inner and outer exits directed downwards. This tunnel shape, as already suggested by some authors, appears to be an effective technical solution to reducing the PC-related complication rates.

  15. Occurrence of myofascial pain in patients with possible carpal tunnel syndrome - a single-blinded study

    DEFF Research Database (Denmark)

    Qerama, Erisela; Kasch, Helge; Fuglsang-Frederiksen, Anders

    2009-01-01

    There exits some similarity between symptoms of carpal tunnel syndrome (CTS) and myofascial pain related to trigger points (TPs) in the infraspinatus muscle.......There exits some similarity between symptoms of carpal tunnel syndrome (CTS) and myofascial pain related to trigger points (TPs) in the infraspinatus muscle....

  16. When does an electron exit a tunneling barrier?

    Directory of Open Access Journals (Sweden)

    Ivanov M. Yu.

    2013-03-01

    Full Text Available We probe the dynamics of tunnel ionization via high harmonic generation. We characterize the ionization dynamics in helium atoms, and apply our approach to resolve subtle differences in ionization from different orbitals of a CO2 molecule.

  17. Free Surface Water Tunnel (FSWT)

    Data.gov (United States)

    Federal Laboratory Consortium — Description: The Free Surface Water Tunnel consists of the intake plenum, the test section and the exit plenum. The intake plenum starts with a perforated pipe that...

  18. Experimental Evidence for Quantum Tunneling Time

    Science.gov (United States)

    Camus, Nicolas; Yakaboylu, Enderalp; Fechner, Lutz; Klaiber, Michael; Laux, Martin; Mi, Yonghao; Hatsagortsyan, Karen Z.; Pfeifer, Thomas; Keitel, Christoph H.; Moshammer, Robert

    2017-07-01

    The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron's classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the "tunnel exit."

  19. Inferior tendon graft to bone tunnel healing at the tibia compared to that at the femur after anterior cruciate ligament reconstruction

    International Nuclear Information System (INIS)

    Lui, P.P.Y.; Ho, G.; Shum, W.T.; Lee, Y.W.; Ho, P.Y.; Lo, W.N.; Lo, C.K.

    2010-01-01

    Tunnel widening after anterior cruciate ligament (ACL) reconstruction (ACLR) is commonly reported without a clear understanding of the mechanism. This study aimed to quantify the spatiotemporal change of the newly formed bone mass, bone tunnel diameter, and area along both bone tunnels using micro-computed tomography (μCT) and correlated the result with histology. ACLR was performed in 24 rabbits. At baseline and weeks 2, 6, and 12, the juxta-articular, middle, and exit segments of both tunnels were harvested for μCT and histological evaluation. μCT and histology revealed significant bone tunnel and graft-bone tunnel healing, respectively, only at week 6 after reconstruction. Despite this, the mean tunnel diameter and area remained relatively unchanged with time. The newly formed bone mass [new bone volume/total bone volume (BV/TV) ratio] and its bone mineral density (BMD) were both higher, whereas the mean tunnel diameter and area were significantly smaller at the femoral tunnel compared to those at the tibial tunnel at weeks 6 and 12 and at week 12, respectively. These were consistent with histological findings, which showed inferior graft remodeling and integration at the tibial tunnel at weeks 6 and 12. The BV/TV increased, whereas the mean tunnel diameter and area decreased toward the exit segment of both tunnels. However, whereas better histological healing occurred at the femoral exit segment, poorer graft remodeling and Sharpey's fiber formation occurred at the tibial exit segment. Poor healing was observed during the initial 6 weeks, particularly that of the tibia, after ACLR. Bone resorption was rapid during healing, resulting in unchanged tunnel diameter and area with time. (author)

  20. Dynamics of tunneling ionization using Bohmian mechanics

    Science.gov (United States)

    Douguet, Nicolas; Bartschat, Klaus

    2018-01-01

    Recent attoclock experiments and theoretical studies regarding the strong-field ionization of atoms by few-cycle infrared pulses revealed features that have attracted much attention. Here we investigate tunneling ionization and the dynamics of the electron probability using Bohmian mechanics. We consider a one-dimensional problem to illustrate the underlying mechanisms of the ionization process. It is revealed that in the major part of the below-the-barrier ionization regime, in an intense and short infrared pulse, the electron does not tunnel through the entire barrier, but rather starts already from the classically forbidden region. Moreover, we highlight the correspondence between the probability of locating the electron at a particular initial position and its asymptotic momentum. Bohmian mechanics also provides a natural definition of mean tunneling time and exit position, taking account of the time dependence of the barrier. Finally, we find that the electron can exit the barrier with significant kinetic energy, thereby corroborating the results of a recent study [N. Camus et al., Phys. Rev. Lett. 119, 023201 (2017), 10.1103/PhysRevLett.119.023201].

  1. A reduced theoretical model for estimating condensation effects in combustion-heated hypersonic tunnel

    Science.gov (United States)

    Lin, L.; Luo, X.; Qin, F.; Yang, J.

    2018-03-01

    As one of the combustion products of hydrocarbon fuels in a combustion-heated wind tunnel, water vapor may condense during the rapid expansion process, which will lead to a complex two-phase flow inside the wind tunnel and even change the design flow conditions at the nozzle exit. The coupling of the phase transition and the compressible flow makes the estimation of the condensation effects in such wind tunnels very difficult and time-consuming. In this work, a reduced theoretical model is developed to approximately compute the nozzle-exit conditions of a flow including real-gas and homogeneous condensation effects. Specifically, the conservation equations of the axisymmetric flow are first approximated in the quasi-one-dimensional way. Then, the complex process is split into two steps, i.e., a real-gas nozzle flow but excluding condensation, resulting in supersaturated nozzle-exit conditions, and a discontinuous jump at the end of the nozzle from the supersaturated state to a saturated state. Compared with two-dimensional numerical simulations implemented with a detailed condensation model, the reduced model predicts the flow parameters with good accuracy except for some deviations caused by the two-dimensional effect. Therefore, this reduced theoretical model can provide a fast, simple but also accurate estimation of the condensation effect in combustion-heated hypersonic tunnels.

  2. Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9

    Directory of Open Access Journals (Sweden)

    Arava Yoav

    2007-08-01

    Full Text Available Abstract Background The yeast ribosomal protein S9 (S9 is located at the entrance tunnel of the mRNA into the ribosome. It is known to play a role in accurate decoding and its bacterial homolog (S4 has recently been shown to be involved in opening RNA duplexes. Here we examined the effects of changing the C terminus of S9, which is rich in acidic amino acids and extends out of the ribosome surface. Results We performed a genome-wide analysis to reveal effects at the transcription and translation levels of all yeast genes. While negligible relative changes were observed in steady-state mRNA levels, a significant number of mRNAs appeared to have altered ribosomal density. Notably, 40% of the genes having reliable signals changed their ribosomal association by more than one ribosome. Yet, no general correlations with physical or functional features of the mRNA were observed. Ribosome Density Mapping (RDM along four of the mRNAs with increased association revealed an increase in ribosomal density towards the end of the coding region for at least two of them. Read-through analysis did not reveal any increase in read-through of a premature stop codon by the mutant strain. Conclusion The ribosomal protein rpS9 appears to be involved in the translation of many mRNAs, since altering its C terminus led to a significant change in ribosomal association of many mRNAs. We did not find strong correlations between these changes and several physical features of the mRNA, yet future studies with advanced tools may allow such correlations to be determined. Importantly, our results indicate an accumulation of ribosomes towards the end of the coding regions of some mRNAs. This suggests an involvement of S9 in ribosomal dissociation during translation termination.

  3. Exit selection strategy in pedestrian evacuation simulation with multi-exits

    International Nuclear Information System (INIS)

    Yue Hao; Zhang Bin-Ya; Shao Chun-Fu; Xing Yan

    2014-01-01

    A mixed strategy of the exit selection in a pedestrian evacuation simulation with multi-exits is constructed by fusing the distance-based and time-based strategies through a cognitive coefficient, in order to reduce the evacuation imbalance caused by the asymmetry of exits or pedestrian layout, to find a critical density to distinguish whether the strategy of exit selection takes effect or not, and to analyze the exit selection results with different cognitive coefficients. The strategy of exit selection is embedded in the computation of the shortest estimated distance in a dynamic parameter model, in which the concept of a jam area layer and the procedure of step-by-step expending are introduced. Simulation results indicate the characteristics of evacuation time gradually varying against cognitive coefficient and the effectiveness of reducing evacuation imbalance caused by the asymmetry of pedestrian or exit layout. It is found that there is a critical density to distinguish whether a pedestrian jam occurs in the evacuation and whether an exit selection strategy is in effect. It is also shown that the strategy of exit selection has no effect on the evacuation process in the no-effect phase with a low density, and that evacuation time and exit selection are dependent on the cognitive coefficient and pedestrian initial density in the in-effect phase with a high density. (general)

  4. The overshoot problem in inflation after tunneling

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Koushik; Vaudrevange, Pascal M.; Westphal, Alexander

    2011-09-15

    We show the absence of the usual parametrically large overshoot problem of small-field inflation if initiated by a Coleman-De Luccia (CDL) tunneling transition from an earlier vacuum in the limit of small inflationary scale compared to the tunneling scale. For low-power monomial exit potentials V({phi}){proportional_to} {phi}{sup n}; n<4, we derive an expression for the amount of overshoot. This is bounded from above by the width of the steep barrier traversed after emerging from tunneling and before reaching a slow-roll region of the potential. For n{>=}4 we show that overshooting is entirely absent. We extend this result through binomials to a general potential written as a series expansion, and to the case of arbitrary finite initial speed of the inflaton. This places the phase space of initial conditions for small-field and large-field inflation on the same footing in a landscape of string theory vacua populated via CDL tunneling. (orig.)

  5. Experimental Evidence for Wigner’s Tunneling Time

    Science.gov (United States)

    Camus, N.; Yakaboylu, E.; Fechner, L.; Klaiber, M.; Laux, M.; Mi, Y.; Hatsagortsyan, K. Z.; Pfeifer, T.; Keitel, C. H.; Moshammer, R.

    2018-04-01

    Tunneling of a particle through a barrier is one of the counter-intuitive properties of quantum mechanical motion. Thanks to advances in the generation of strong laser fields, new opportunities to dynamically investigate this process have been developed. In the so-called attoclock measurements the electron’s properties after tunneling are mapped on its emission direction. We investigate the tunneling dynamics and achieve a high sensitivity thanks to two refinements of the attoclock principle. Using near-IR wavelength we place firmly the ionization process in the tunneling regime. Furthermore, we compare the electron momentum distributions of two atomic species of slightly different atomic potentials (argon and krypton) being ionized under absolutely identical conditions. Experimentally, using a reaction microscope, we succeed in measuring the 3D electron momentum distributions for both targets simultaneously. Theoretically, the time resolved description of tunneling in strong-field ionization is studied using the leading quantum-mechanical Wigner treatment. A detailed analysis of the most probable photoelectron emission for Ar and Kr allows testing the theoretical models and a sensitive check of the electron initial conditions at the tunnel exit. The agreement between experiment and theory provides a clear evidence for a non-zero tunneling time delay and a non-vanishing longitudinal momentum at this point.

  6. Exit from contract

    Directory of Open Access Journals (Sweden)

    Oren Bar-Gill

    2016-01-01

    Full Text Available Objective to study the procedure of exiting the contract its costs and benefits. Methods statistical method comparative analysis. Results free exit from contract is one of the most powerful tools for the consumer rights protection. The procedure frees consumers from bad deals and keeps businesses honest. Yet consumers often choose transactions with lockin provisions trading off exit rights for other perks. This article examines the costs and benefits of free exit as compared to the lockin alternative. According to the authors the present regulation of exit penalties in the USA is poorly tailored to address concerns about lockin particularly in light of increasingly ubiquitous marketbased solutions. The article also calls regulatory attention to loyalty rewards which are shown to be as powerful as exit penalties and equally detrimental. Scientific novelty the article reveals a paradoxical state of the law exit regulations in the USA are used most where they are needed least. Termination penalties present an obvishyous target for regulatory intervention while loyalty programs seem benign not warranting any regulatory attention. Practical significance the article is of interest for the Russian juridical science and lawmaking authorities as in Russia the issue of exiting the contract is as topical as in the USA and requires solution which would impair neither the rights of consumers nor the rights of the sellers ofnbspproducts and services. nbsp

  7. Exit-strategies

    DEFF Research Database (Denmark)

    Mørck, Line Lerche; Palm, Anne-Mette; Sys Møller-Andersen, Camilla

    different empirical sources. To develop and extend an "exit-prototype" about conditions of importance for moving beyond a gang/criminal position, we have analyzed documents (from newspapers and books), involved ex-gang members, social workers and experts as co-researchers in interviews, "gang......This paper is about exit-strategies, constructing a theoretical and empirical informed analysis of current societal conditions that influence motor cycle gangs such as Hells Angels or Bandidos and other ‘wild' youth' possibilities and limitations for moving beyond criminal activities. We especially...... focus on the involved communities in the current Danish gang-conflict, which escalated with deadly killings in 2008, and thereby became a so called "gang-war". We will start out presenting different practice notions of exit, and we will extend and discuss understandings of "exit-strategies" by analyzing...

  8. Stability Analysis of Tunnel-Slope Coupling Based on Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Tao Luo

    2015-07-01

    Full Text Available Subjects in tunnels, being constrained by terrain and routes, entrances and exits to tunnels, usually stay in the terrain with slopes. Thus, it is necessary to carry out stability analysis by treating the tunnel slope as an entity. In this study, based on the Janbu slices method, a model for the calculation of the stability of the original slope-tunnel-bank slope is established. The genetic algorithm is used to implement calculation variables, safety coefficient expression and fitness function design. The stability of the original slope-tunnel-bank slope under different conditions is calculated, after utilizing the secondary development function of the mathematical tool MATLAB for programming. We found that the bearing capacity of the original slopes is reduced as the tunnels are excavated and the safety coefficient is gradually decreased as loads of the embankment construction increased. After the embankment was constructed, the safety coefficient was 1.38, which is larger than the 1.3 value specified by China’s standards. Thus, the original slope-tunnel-bank slope would remain in a stable state.

  9. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.

    Science.gov (United States)

    Boehringer, Daniel; Thermann, Rolf; Ostareck-Lederer, Antje; Lewis, Joe D; Stark, Holger

    2005-11-01

    Initiation of translation of the hepatitis C virus (HCV) polyprotein is driven by an internal ribosome entry site (IRES) RNA that bypasses much of the eukaryotic translation initiation machinery. Here, single-particle electron cryomicroscopy has been used to study the mechanism of HCV IRES-mediated initiation. A HeLa in vitro translation system was used to assemble human IRES-80S ribosome complexes under near physiological conditions; these were stalled before elongation. Domain 2 of the HCV IRES is bound to the tRNA exit site, touching the L1 stalk of the 60S subunit, suggesting a mechanism for the removal of the HCV IRES in the progression to elongation. Domain 3 of the HCV IRES positions the initiation codon in the ribosomal mRNA binding cleft by binding helix 28 at the head of the 40S subunit. The comparison with the previously published binary 40S-HCV IRES complex reveals structural rearrangements in the two pseudoknot structures of the HCV IRES in translation initiation.

  10. Exit Prostitution

    DEFF Research Database (Denmark)

    Henriksen, Theresa Dyrvig; Aslaug Kjær, Agnete; Christensen, Gunvor

    2015-01-01

    Dette midtvejsnotat omhandler projektet ”Exit prostitution”. Exit-projektet blev påbegyndt i april 2012 og løber til udgangen af 2015 og befinder sig i øjeblikket midtvejs i projektets afprøvningsfase. I projektet anvendes metoden Critical Time Intervention (CTI), der er en evidensbaseret...... til det. Exit-projektet er dermed en central socialpolitisk indsats overfor borgere i prostitution i det danske samfund. I dette notat belyser vi midtvejsresultater for, hvordan udviklingen er for de borgere, der er nået halvt igennem et CTI-forløb. I den afsluttende evaluering af projektet i 2015 vil...

  11. Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.

    Science.gov (United States)

    Jomaa, Ahmad; Boehringer, Daniel; Leibundgut, Marc; Ban, Nenad

    2016-01-25

    Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon. Our results reveal the conformational changes that regulate the latching of the signal sequence, the release of the heterodimeric domains of the signal recognition particle and its receptor, and the handover of the signal sequence to the translocon. We also observe that the signal recognition particle and the translocon insert-specific structural elements into the ribosomal tunnel to remodel it, possibly to sense nascent chains. Our work provides structural evidence for a conformational state of the signal recognition particle and its receptor primed for translocon binding to the ribosome-nascent chain complex.

  12. Ribosomal protein methyltransferases in the yeast Saccharomyces cerevisiae: Roles in ribosome biogenesis and translation.

    Science.gov (United States)

    Al-Hadid, Qais; White, Jonelle; Clarke, Steven

    2016-02-12

    A significant percentage of the methyltransferasome in Saccharomyces cerevisiae and higher eukaryotes is devoted to methylation of the translational machinery. Methylation of the RNA components of the translational machinery has been studied extensively and is important for structure stability, ribosome biogenesis, and translational fidelity. However, the functional effects of ribosomal protein methylation by their cognate methyltransferases are still largely unknown. Previous work has shown that the ribosomal protein Rpl3 methyltransferase, histidine protein methyltransferase 1 (Hpm1), is important for ribosome biogenesis and translation elongation fidelity. In this study, yeast strains deficient in each of the ten ribosomal protein methyltransferases in S. cerevisiae were examined for potential defects in ribosome biogenesis and translation. Like Hpm1-deficient cells, loss of four of the nine other ribosomal protein methyltransferases resulted in defects in ribosomal subunit synthesis. All of the mutant strains exhibited resistance to the ribosome inhibitors anisomycin and/or cycloheximide in plate assays, but not in liquid culture. Translational fidelity assays measuring stop codon readthrough, amino acid misincorporation, and programmed -1 ribosomal frameshifting, revealed that eight of the ten enzymes are important for translation elongation fidelity and the remaining two are necessary for translation termination efficiency. Altogether, these results demonstrate that ribosomal protein methyltransferases in S. cerevisiae play important roles in ribosome biogenesis and translation. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Phase Structure of Strong-Field Tunneling Wave Packets from Molecules.

    Science.gov (United States)

    Liu, Ming-Ming; Li, Min; Wu, Chengyin; Gong, Qihuang; Staudte, André; Liu, Yunquan

    2016-04-22

    We study the phase structure of the tunneling wave packets from strong-field ionization of molecules and present a molecular quantum-trajectory Monte Carlo model to describe the laser-driven dynamics of photoelectron momentum distributions of molecules. Using our model, we reproduce and explain the alignment-dependent molecular frame photoelectron spectra of strong-field tunneling ionization of N_{2} reported by M. Meckel et al. [Nat. Phys. 10, 594 (2014)]. In addition to modeling the low-energy photoelectron angular distributions quantitatively, we extract the phase structure of strong-field molecular tunneling wave packets, shedding light on its physical origin. The initial phase of the tunneling wave packets at the tunnel exit depends on both the initial transverse momentum distribution and the molecular internuclear distance. We further show that the ionizing molecular orbital has a critical effect on the initial phase of the tunneling wave packets. The phase structure of the photoelectron wave packet is a key ingredient for modeling strong-field molecular photoelectron holography, high-harmonic generation, and molecular orbital imaging.

  14. Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome

    Science.gov (United States)

    Poirot, Olivier; Timsit, Youri

    2016-05-01

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

  15. Exit prostitution

    DEFF Research Database (Denmark)

    Mehlsen, Line; Aslaug Kjær, Agnete; Amilon, Anna

    2016-01-01

    Dette statusnotat for projektet ”Exit Prostitution” belyser de foreløbige resultater og tendenser for projektet. Exit Prostitution løb oprindeligt fra april 2012 til udgangen af 2015, men med en nylig forlængelse løber projektet til udgangen af 2016. Projektet befinder sig således i slutningen af...... afprøvet med succes i forhold til hjemløshed både nationalt og internationalt. Målet med anvendelsen af metoden i forhold til målgruppen for Exit Prostitution er, at borgere med prostitutionserfaring, som ønsker at ophøre med salg af seksuelle ydelser eller ønsker at opleve en forbedring af deres...

  16. New model for mines and transportation tunnels external dose calculation using Monte Carlo simulation

    International Nuclear Information System (INIS)

    Allam, Kh. A.

    2017-01-01

    In this work, a new methodology is developed based on Monte Carlo simulation for tunnels and mines external dose calculation. Tunnels external dose evaluation model of a cylindrical shape of finite thickness with an entrance and with or without exit. A photon transportation model was applied for exposure dose calculations. A new software based on Monte Carlo solution was designed and programmed using Delphi programming language. The variation of external dose due to radioactive nuclei in a mine tunnel and the corresponding experimental data lies in the range 7.3 19.9%. The variation of specific external dose rate with position in, tunnel building material density and composition were studied. The given new model has more flexible for real external dose in any cylindrical tunnel structure calculations. (authors)

  17. Attoclock reveals natural coordinates of the laser-induced tunnelling current flow in atoms

    DEFF Research Database (Denmark)

    Pfeiffer, Adrian N.; Cirelli, Claudio; Smolarski, Mathias

    2012-01-01

    the attoclock technique4 to obtain experimental information about the electron tunnelling geometry (the natural coordinates of the tunnelling current flow) and exit point. We confirm vanishing tunnelling delay time, show the importance of the inclusion of Stark shifts5, 6 and report on multi-electron effects......In the research area of strong-laser-field interactions and attosecond science1, tunnelling of an electron through the barrier formed by the electric field of the laser and the atomic potential is typically assumed to be the initial key process that triggers subsequent dynamics1, 2, 3. Here we use...... clearly identified by comparing results in argon and helium atoms. Our combined theory and experiment allows us to single out the geometry of the inherently one-dimensional tunnelling problem, through an asymptotic separation of the full three-dimensional problem. Our findings have implications for laser...

  18. Design and analysis of the tunnel connecting the beam corridor and the spectrum hall of the CSNS

    International Nuclear Information System (INIS)

    Liu Jian; Wang Qingbin; Wu Qingbiao; Ma Zhongjian

    2011-01-01

    There is a tunnel connecting the beamcorridor and the target station in the spectrum hall in the CSNS project. The length of the tunnel is about 20 m. The shielding design of the tunnel is very significant for the persons working in the spectrum hall because the tunnel is not covered by soil for shielding. In order to reduce the dose rate at the exit of the cable ducts, we use the ISIS construction, which is designed with four turnings, as a reference for the tunnel design. The thickness of the shielding is obtained by a simulation with the Monte Carlo Code FLUKA. The result is compared with the data obtained with Moyer Mode and the reliability of the simulation is proved. This paper provides the basis for the design of the tunnel. (authors)

  19. Comparison of acoustic data from a 102 mm conic nozzle as measured in the RAE 24-foot wind tunnel and the NASA Ames 40- by 80-foot wind tunnel

    Science.gov (United States)

    Atencio, A., Jr.; Mckie, J.

    1982-01-01

    A cooperative program between the Royal Aircraft Establishment (RAE), England, and the NASA Ames Research Center was initiated to compare acoustic measurements made in the RAE 24-foot wind tunnel and in the Ames 40- by 80-foot wind tunnel. The acoustic measurements were made in both facilities using the same 102 mm conical nozzle supplied by the RAE. The nozzle was tested by each organization using its respective jet test rig. The mounting hardware and nozzle exit conditions were matched as closely as possible. The data from each wind tunnel were independently analyzed by the respective organization. The results from these tests show good agreement. In both facilities, interference with acoustic measurement is evident at angles in the forward quadrant.

  20. Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis.

    Science.gov (United States)

    Moriggi, Giulia; Nieto, Blanca; Dosil, Mercedes

    2014-12-01

    During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.

  1. Fluorescence Imaging of Rotational and Vibrational Temperature in a Shock Tunnel Nozzle Flow

    Science.gov (United States)

    Palma, Philip C.; Danehy, Paul M.; Houwing, A. F. P.

    2003-01-01

    Two-dimensional rotational and vibrational temperature measurements were made at the nozzle exit of a free-piston shock tunnel using planar laser-induced fluorescence. The Mach 7 flow consisted predominantly of nitrogen with a trace quantity of nitric oxide. Nitric oxide was employed as the probe species and was excited at 225 nm. Nonuniformities in the distribution of nitric oxide in the test gas were observed and were concluded to be due to contamination of the test gas by driver gas or cold test gas.The nozzle-exit rotational temperature was measured and is in reasonable agreement with computational modeling. Nonlinearities in the detection system were responsible for systematic errors in the measurements. The vibrational temperature was measured to be constant with distance from the nozzle exit, indicating it had frozen during the nozzle expansion.

  2. Characterization of a new open jet wind tunnel to optimize and test vertical axis wind turbines

    DEFF Research Database (Denmark)

    Tourn, Silvana; Pallarès, Jordi; Cuesta, Ildefonso

    2017-01-01

    Based on the increasing interest in urban environmental technologies, the study of small scale vertical axis wind turbines shows motivating challenges. In this paper, we present the characteristics and potentials of a new open jet wind tunnel. It has a nozzle exit area of 1.5 × 1.5 m2, and it can......%. The detailed characterization of the flow carried out indicates that the wind tunnel can be used to test small scale models of wind turbines....

  3. Probing the longitudinal momentum spread of the electron wave packet at the tunnel exit

    DEFF Research Database (Denmark)

    N. Pfeiffer, Adrian; Cirelli, Claudio; S. Landsman, Alexandra

    2012-01-01

    We present an ellipticity resolved study of momentum distributions arising from strong-field ionization of Helium at constant intensity. The influence of the ion potential on the departing electron is considered within a semi-classical model consisting of an initial tunneling step and subsequent...

  4. 29 CFR 1917.122 - Employee exits.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Employee exits. 1917.122 Section 1917.122 Labor Regulations...) MARINE TERMINALS Terminal Facilities § 1917.122 Employee exits. (a) Employee exits shall be clearly marked. (b) If an employee exit is not visible from employees' work stations, directional signs...

  5. 5S rRNA and ribosome.

    Science.gov (United States)

    Gongadze, G M

    2011-12-01

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

  6. In vitro degradation of ribosomes.

    Science.gov (United States)

    Mora, G; Rivas, A

    1976-12-01

    The cytoplasmic ribosomes from Euglena gracilis var. bacillaris are found to be of two types taking into consideration their stability "in vitro". In the group of unstable ribosomes the large subunit is degraded. The other group apparently does not suffer any degradation under the conditions described. However the RNAs extracted from both types of ribosomes are degraded during sucrose density gradients. The degradation of the largest RNA species has been reported previously, but no comment has been made about the stability of the ribosome itself.

  7. Exit Polls and Voter Turnout

    DEFF Research Database (Denmark)

    Andersen, Asger Lau; Jensen, Thomas

    2014-01-01

    After the 2009 referendum on a proposed change to the Danish Law of Succession, it was widely claimed that the early publication of exit poll results changed the rate of turnout and eventually the outcome. We investigate this claim and contribute to the wider debate on the implications of exit...... polls by setting up and analyzing a formal model. We find that the introduction of an exit poll influences the incentive to vote both before and after the poll is published, but the signs of the effects are generally ambiguous. The observation that exit polls influence the incentive to vote even before...

  8. Ribosomal studies on the 70S ribosome of E.coli by means of neutron scattering

    International Nuclear Information System (INIS)

    Burkhardt, N.

    1997-01-01

    Ribosomes are ribonucleo-protein complexes, which catalyse proteinbiosynthesis in all living organisms. Currently, most of the structural models of the prokaryotic 70S ribosome rely on electron microscopy and describe mainly the outer shape of the particle. Neutron scattering can provide information on the internal structure of the ribosome. Parts of the structure can be contrasted for neutrons by means of an isotopic exchange of the naturally occurring hydrogen ( 1 H) for deuterium ( 2 H), allowing direct measurements in situ. Specifically deuterium-labeled ribosomes (E. coli) were prepared and analysed with neutron scattering. The biochemical methods were established and combined to a generally applicable preparation system. This allows labeling of all ribosomal components in any combination. A systematic analysis of the protein and RNA phases resulted in the development of a new model for the 70S ribosome. This model describes not only the outer shape of the particle, but displays also an experimentally determined internal protein-RNA distribution and the border of subunits for the first time (four-phase model; resolution: 50A). Models of the 70S ribosome from other studies were evaluated and ranked according to consistency with the measured scattering data. Applying a new neutron scattering technique of particular sensitivity, the proton-spin contrast-variation, single proteins could be measured and localized. The positions of the proteins S6 and S10 were determined, providing the first coordinates of protein mass centers within the 70S ribosome. (orig.) [de

  9. Detection and Quantification of Ribosome Inhibition by Aminoglycoside Antibiotics in Living Bacteria Using an Orthogonal Ribosome-Controlled Fluorescent Reporter.

    Science.gov (United States)

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

    2016-01-15

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

  10. Energy Optimization of Road Tunnel Lighting Systems

    Directory of Open Access Journals (Sweden)

    Ferdinando Salata

    2015-07-01

    Full Text Available A road tunnel is an enclosed and covered infrastructure for the vehicular traffic. Its lighting system provides 24 h of artificial sources only, with a higher amount of electric power used during the day. Due to safety reasons, when there is natural lighting outside the tunnel, the lighting levels in the stretches right after the entrance and before the exit must be high, in order to guide the driver’s eye towards the middle of the tunnel where the luminance must guarantee safe driving, avoid any over-dimensioning of the lighting systems, and produce energy savings. Such effects can be reached not only through the technological advances in the field of artificial lighting sources with high luminous efficiency, but also through new materials for road paving characterized by a higher reflection coefficient than other ordinary asphalts. This case study examines different technical scenarios, analyzing and comparing possible energy and economic savings. Traditional solutions are thus compared with scenarios suggesting the solutions previously mentioned. Special asphalts are interesting from an economic point of view, whereas the high costs of LED sources nowadays represent an obstacle for their implementation.

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

    Directory of Open Access Journals (Sweden)

    Bani Kumar Pathak

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

  12. Firm Exit, Technological Progress and Trade

    DEFF Research Database (Denmark)

    Schröder, Philipp; Sørensen, Allan

    The dynamics of export market exit and firm closure have found limited attention in the new heterogeneous-firms trade literature. In fact, several of the predictions on firm survival and exit stemming from this new class of models are at odds with the stylized facts. Empirically, higher productiv......The dynamics of export market exit and firm closure have found limited attention in the new heterogeneous-firms trade literature. In fact, several of the predictions on firm survival and exit stemming from this new class of models are at odds with the stylized facts. Empirically, higher...... productivity firms survive longer, most firm closures are young firms, higher productivity exporters are more likely to continue to export compared to less productive exporters and market exits as well as firm closures are typically preceded by periods of contracting market shares. The present paper shows...... liberalization on export market exit and firm closure....

  13. Vanillin inhibits translation and induces messenger ribonucleoprotein (mRNP) granule formation in saccharomyces cerevisiae: application and validation of high-content, image-based profiling.

    Science.gov (United States)

    Iwaki, Aya; Ohnuki, Shinsuke; Suga, Yohei; Izawa, Shingo; Ohya, Yoshikazu

    2013-01-01

    Vanillin, generated by acid hydrolysis of lignocellulose, acts as a potent inhibitor of the growth of the yeast Saccharomyces cerevisiae. Here, we investigated the cellular processes affected by vanillin using high-content, image-based profiling. Among 4,718 non-essential yeast deletion mutants, the morphology of those defective in the large ribosomal subunit showed significant similarity to that of vanillin-treated cells. The defects in these mutants were clustered in three domains of the ribosome: the mRNA tunnel entrance, exit and backbone required for small subunit attachment. To confirm that vanillin inhibited ribosomal function, we assessed polysome and messenger ribonucleoprotein granule formation after treatment with vanillin. Analysis of polysome profiles showed disassembly of the polysomes in the presence of vanillin. Processing bodies and stress granules, which are composed of non-translating mRNAs and various proteins, were formed after treatment with vanillin. These results suggest that vanillin represses translation in yeast cells.

  14. Promoting Exit from Violent Extremism

    DEFF Research Database (Denmark)

    Dalgaard-Nielsen, Anja

    2013-01-01

    A number of Western countries are currently adding exit programs targeting militant Islamists to their counterterrorism efforts. Drawing on research into voluntary exit from violent extremism, this article identifies themes and issues that seem to cause doubt, leading to exit. It then provides a ...... the influence attempt as subtle as possible, use narratives and self-affirmatory strategies to reduce resistance to persuasion, and consider the possibility to promote attitudinal change via behavioral change as an alternative to seek to influence beliefs directly....

  15. A ribosome without RNA

    Directory of Open Access Journals (Sweden)

    Harold S Bernhardt

    2015-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Monique N O'Leary

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

  17. Synthetic peptides and ribosomal proteins as substrate for 60S ribosomal protein kinase from yeast cells

    DEFF Research Database (Denmark)

    Grankowski, N; Gasior, E; Issinger, O G

    1993-01-01

    Kinetic studies on the 60S protein kinase were conducted with synthetic peptides and ribosomal proteins as substrate. Peptide RRREEESDDD proved to be the best synthetic substrate for this enzyme. The peptide has a sequence of amino acids which most closely resembles the structure of potential...... phosphorylation sites in natural substrates, i.e., acidic ribosomal proteins. The superiority of certain kinetic parameters for 60S kinase obtained with the native whole 80S ribosomes over those of the isolated fraction of acidic ribosomal proteins indicates that the affinity of 60S kinase to the specific protein...

  18. ANALYSIS OF FACTORS CAUSING WATER DAMAGE TO LOESS DOUBLE-ARCHED TUNNEL BASED ON TFN-AHP

    Directory of Open Access Journals (Sweden)

    Mao Zheng-jun

    2017-04-01

    Full Text Available In order to analysis the factors causing water damage to loess double-arched tunnel, this paper conducts field investigation on water damage to tunnels on Lishi-Jundu Expressway in Shanxi, China, confirms its development characteristics, builds an index system (covering 36 evaluation indexes for construction condition, design stage, construction stage, and operation stage for the factors causing water damage to loess double-arched tunnel, applies TFN-AHP (triangular fuzzy number-analytic hierarchy process in calculating the weight of indexes at different levels, and obtains the final sequence of weight of the factors causing water seepage to loess double-arched tunnel. It is found out that water damage to loess double-arched tunnel always develops in construction joints, expansion joints, settlement joints, and lining joints of tunnel and even around them; there is dotted water seepage, linear water seepage, and planar water seepage according to the trace and scope of water damage to tunnel lining. The result shows that water damage to loess double-arched tunnel mainly refers to linear water seepage, planar water seepage is also developed well, and partition and equipment box at the entrance and exit of tunnel are prone to water seepage; construction stage is crucial for controlling water damage to loess double-arched tunnel, atmospheric precipitation is the main water source, and the structure defect of double-arched tunnel increases the possibility of water seepage; the final sequence for weight of various factors is similar to the actual result.

  19. Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.

    Science.gov (United States)

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

    2015-10-06

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

  20. Ribosomal studies on the 70S ribosome of E.coli by means of neutron scattering; Strukturuntersuchungen am 70S-Ribosom von E.coli unter Anwendung von Neutronenstreuung

    Energy Technology Data Exchange (ETDEWEB)

    Burkhardt, N. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Werkstofforschung

    1997-12-31

    Ribosomes are ribonucleo-protein complexes, which catalyse proteinbiosynthesis in all living organisms. Currently, most of the structural models of the prokaryotic 70S ribosome rely on electron microscopy and describe mainly the outer shape of the particle. Neutron scattering can provide information on the internal structure of the ribosome. Parts of the structure can be contrasted for neutrons by means of an isotopic exchange of the naturally occurring hydrogen ({sup 1}H) for deuterium ({sup 2}H), allowing direct measurements in situ. Specifically deuterium-labeled ribosomes (E. coli) were prepared and analysed with neutron scattering. The biochemical methods were established and combined to a generally applicable preparation system. This allows labeling of all ribosomal components in any combination. A systematic analysis of the protein and RNA phases resulted in the development of a new model for the 70S ribosome. This model describes not only the outer shape of the particle, but displays also an experimentally determined internal protein-RNA distribution and the border of subunits for the first time (four-phase model; resolution: 50A). Models of the 70S ribosome from other studies were evaluated and ranked according to consistency with the measured scattering data. Applying a new neutron scattering technique of particular sensitivity, the proton-spin contrast-variation, single proteins could be measured and localized. The positions of the proteins S6 and S10 were determined, providing the first coordinates of protein mass centers within the 70S ribosome. (orig.) [Deutsch] Ribosomen sind Ribonukleinsaeure-Protein Komplexe, die in allen lebenden Organismen die Proteinbiosynthese katalysieren. Strukturmodelle fuer das prokaryontische 70S-Ribosom beruhen derzeit vorwiegend auf elektronenmikroskopischen Untersuchungen und beschreiben im wesentlichen die aeussere Oberflaeche des Partikels. Informationen ueber die innere Struktur des Ribosoms koennen Messungen mit

  1. Ribosomal studies on the 70S ribosome of E.coli by means of neutron scattering; Strukturuntersuchungen am 70S-Ribosom von E.coli unter Anwendung von Neutronenstreuung

    Energy Technology Data Exchange (ETDEWEB)

    Burkhardt, N [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Werkstofforschung

    1998-12-31

    Ribosomes are ribonucleo-protein complexes, which catalyse proteinbiosynthesis in all living organisms. Currently, most of the structural models of the prokaryotic 70S ribosome rely on electron microscopy and describe mainly the outer shape of the particle. Neutron scattering can provide information on the internal structure of the ribosome. Parts of the structure can be contrasted for neutrons by means of an isotopic exchange of the naturally occurring hydrogen ({sup 1}H) for deuterium ({sup 2}H), allowing direct measurements in situ. Specifically deuterium-labeled ribosomes (E. coli) were prepared and analysed with neutron scattering. The biochemical methods were established and combined to a generally applicable preparation system. This allows labeling of all ribosomal components in any combination. A systematic analysis of the protein and RNA phases resulted in the development of a new model for the 70S ribosome. This model describes not only the outer shape of the particle, but displays also an experimentally determined internal protein-RNA distribution and the border of subunits for the first time (four-phase model; resolution: 50A). Models of the 70S ribosome from other studies were evaluated and ranked according to consistency with the measured scattering data. Applying a new neutron scattering technique of particular sensitivity, the proton-spin contrast-variation, single proteins could be measured and localized. The positions of the proteins S6 and S10 were determined, providing the first coordinates of protein mass centers within the 70S ribosome. (orig.) [Deutsch] Ribosomen sind Ribonukleinsaeure-Protein Komplexe, die in allen lebenden Organismen die Proteinbiosynthese katalysieren. Strukturmodelle fuer das prokaryontische 70S-Ribosom beruhen derzeit vorwiegend auf elektronenmikroskopischen Untersuchungen und beschreiben im wesentlichen die aeussere Oberflaeche des Partikels. Informationen ueber die innere Struktur des Ribosoms koennen Messungen mit

  2. Differential Stoichiometry among Core Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Nikolai Slavov

    2015-11-01

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

  3. Control of ribosome formation in rat heart

    International Nuclear Information System (INIS)

    Russo, L.A.

    1987-01-01

    Diabetes of 9 days duration produced a 17% diminution in the rate of total protein synthesis in rat hearts perfused as Langendorff preparations supplied with glucose, plasma levels of amino acids, and 400 μU/ml insulin. This reduction was attributable to a decrease in efficiency of protein synthesis and total RNA content. Total messenger RNA content decreased in diabetic hearts in proportion to the reduction in total RNA. Diabetes also resulted in diminished ribosome content as reflected by the induction in total RNA. Ribosome production was investigated by monitoring incorporation of [ 3 H]phenylalanine into the proteins of cytoplasmic ribosomes. Rates of ribosome formation in diabetic hearts were as fast as control rates in the presence of insulin, and were faster than control rates in the absence of the hormone. These results indicated that ribosome content fell in diabetic hearts despite unchanged or faster rates of ribosome formation

  4. Spoiled Onions: Exposing Malicious Tor Exit Relays

    OpenAIRE

    Winter, Philipp; Lindskog, Stefan

    2014-01-01

    Several hundred Tor exit relays together push more than 1 GiB/s of network traffic. However, it is easy for exit relays to snoop and tamper with anonymised network traffic and as all relays are run by independent volunteers, not all of them are innocuous. In this paper, we seek to expose malicious exit relays and document their actions. First, we monitored the Tor network after developing a fast and modular exit relay scanner. We implemented several scanning modules for detecting common attac...

  5. Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution

    DEFF Research Database (Denmark)

    Greber, Basil J; Boehringer, Daniel; Godinic-Mikulcic, Vlatka

    2012-01-01

    additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter...... between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes......, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea....

  6. Understanding international exit from a non-economic and emotional perspective: the case of Taiwanese entrepreneurs exit China

    OpenAIRE

    Lin, Yangpei

    2015-01-01

    I investigate why Taiwanese entrepreneurs who have invested in China exit. Viewed from the non-economic perspective, there are three main themes in this thesis. Theme A focuses on the non-economic variables in international exit. Theme B examines how incident-generated emotions shape entrepreneur’s actions in internationalization. Theme C presents an overview of the decision-making of international exit, summarizing the finding in Theme A and Theme B and revisiting the theor...

  7. Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.

    Science.gov (United States)

    Fuchs, Gabriele; Petrov, Alexey N; Marceau, Caleb D; Popov, Lauren M; Chen, Jin; O'Leary, Seán E; Wang, Richard; Carette, Jan E; Sarnow, Peter; Puglisi, Joseph D

    2015-01-13

    Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.

  8. Crystallization of ribosomes from Thermus thermophilus

    International Nuclear Information System (INIS)

    Karpova, E.A.; Serdyuk, I.N.; Tarkhovskii, Yu.S.; Orlova, E.V.; Borovyagin, V.L.

    1987-01-01

    An understanding of the molecular bases of the process of protein biosynthesis on the ribosome requires a knowledge of its structure with high three-dimensional resolution involving the method of x-ray crystallographic analysis. The authors report on the production of crystals of the 70S ribosomes from a new source - the highly thermophilic bacterium Thermus thermophilus. Ribosomes for crystallization were obtained from Th. thermophilus strain HB8 by two washings in buffer with high ionic strength. The ribosome preparation was investigated for homogeneity by the method of high-speed sedimentation in a buffer containing 15 mM MgCl 2 , 50 mM NH 4 Cl, and 10 MM Tris-HCl, pH 7.5. Analysis showed that the preparation if homogeneous. The same preparation was investigated for intactness of ribosomal RNA by the method of gel electrophoresis in 2.75% acrylamide 0.5% agarose gel in a buffer containing 30 mM Tris, 30 mM NaH 2 PO 4 , 10 mM EDTA, 1-2% SDS, and 6 M urea. Analysis showed that the preparation possesses intact 16S and 23S RNA. The latter did not degrade, at least in a week of exposure of the ribosomes in buffer solution at 5 0 C. The ribosome preparation had no appreciable RNase activity, which was verified by incubating 4.5 micrograms of ribosomes with 3 micrograms of 14 C-labeled 16S rRna (50 0 C, 90 min) in a buffer containing 10 mM MgCl 2 , 100 mM NH 4 Cl, and 10 mM Tris-HCl, pH/sub 20 0 / 7.5. The incubated nonhydrolyzed RNA was precipitated with 5% trichloroacetic acid and applied on a GF/C filter. The radioactivity was determined in a toluene scintillator on an LS-100C counter

  9. New Hypersonic Shock Tunnel at the Laboratory of Aerothermodynamics and Hypersonics Prof. Henry T. Nagamatsu

    International Nuclear Information System (INIS)

    Toro, P. G. P.; Minucci, M. A. S.; Chanes, J. B. Jr; Oliveira, A. C.; Gomes, F. A. A.; Myrabo, L. N.; Nagamatsu, Henry T.

    2008-01-01

    The new 0.60-m. nozzle exit diameter hypersonic shock tunnel was designed to study advanced air-breathing propulsion system such as supersonic combustion and/or laser technologies. In addition, it may be used for hypersonic flow studies and investigations of the electromagnetic (laser) energy addition for flow control. This new hypersonic shock tunnel was designed and installed at the Laboratory for of Aerothermodynamics and Hypersonics Prof. Henry T. Nagamatsu, IEAv-CTA, Brazil. The design of the tunnel enables relatively long test times, 2-10 milliseconds, suitable for the experiments performed at the laboratory. Free stream Mach numbers ranging from 6 to 25 can be produced and stagnation pressures and temperatures up to 360 atm. and up to 9,000 K, respectively, can be generated. Shadowgraph and schlieren optical techniques will be used for flow visualization

  10. Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 and Implications for Ribosome Evolution

    Science.gov (United States)

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

    2013-01-01

    Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea. PMID:22306461

  11. 14 CFR 25.809 - Emergency exit arrangement.

    Science.gov (United States)

    2010-01-01

    ... moveable door or hatch in the external walls of the fuselage, allowing an unobstructed opening to the... event of failure of the primary system. Manual operation of the exit (after failure of the primary... during flight. (i) Each emergency exit must have a means to retain the exit in the open position, once...

  12. Editorial Commentary: The All-Epiphyseal Anterior Cruciate Ligament Distal Femoral Approach: Sockets or Tunnels?

    Science.gov (United States)

    Cordasco, Frank A

    2018-05-01

    I believe that the distal femoral approach for anterior cruciate ligament reconstruction in the skeletally immature athlete with 3 to 6 years of remaining growth is best performed with an all-inside, all-epiphyseal technique using sockets rather than an outside-in approach creating tunnels. A shorter socket rather than a longer tunnel exposes a smaller surface area of the lateral distal femoral physis to potential compromise and resultant valgus malalignment. In addition, exiting the lateral femoral aspect of the epiphysis with a full-diameter tunnel as compared with a smaller diameter drill hole used to prepare a socket places the posterior articular cartilage, the lateral collateral ligament and anterolateral ligament footprints, and the popliteus tendon insertion at risk. My preference for sockets is also related to my belief that they provide a superior biologic milieu for graft incorporation compared with a full-length tunnel with the attendant violation of the lateral femoral cortex of the epiphysis. Copyright © 2018 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  13. Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.

    Science.gov (United States)

    Eichmann, Cédric; Preissler, Steffen; Riek, Roland; Deuerling, Elke

    2010-05-18

    The folding of proteins in living cells may start during their synthesis when the polypeptides emerge gradually at the ribosomal exit tunnel. However, our current understanding of cotranslational folding processes at the atomic level is limited. We employed NMR spectroscopy to monitor the conformation of the SH3 domain from alpha-spectrin at sequential stages of elongation via in vivo ribosome-arrested (15)N,(13)C-labeled nascent polypeptides. These nascent chains exposed either the entire SH3 domain or C-terminally truncated segments thereof, thus providing snapshots of the translation process. We show that nascent SH3 polypeptides remain unstructured during elongation but fold into a compact, native-like beta-sheet assembly when the entire sequence information is available. Moreover, the ribosome neither imposes major conformational constraints nor significantly interacts with exposed unfolded nascent SH3 domain moieties. Our data provide evidence for a domainwise folding of the SH3 domain on ribosomes without significant population of folding intermediates. The domain follows a thermodynamically favorable pathway in which sequential folding units are stabilized, thus avoiding kinetic traps during the process of cotranslational folding.

  14. Source apportionment of traffic emissions of particulate matter using tunnel measurements

    Science.gov (United States)

    Lawrence, Samantha; Sokhi, Ranjeet; Ravindra, Khaiwal; Mao, Hongjun; Prain, Hunter Douglas; Bull, Ian D.

    2013-10-01

    This study aims to quantify exhaust/non-exhaust emissions and the uncertainties associated with them by combining innovative motorway tunnel sampling and source apportionment modelling. Analytical techniques ICP-AES and GC-MS were used to identify the metallic and organic composition of PM10, respectively. Good correlation was observed between Fe, Cu, Mn, Ni, Pb and Sb and change in traffic volume. The concentration of polycyclic aromatic hydrocarbons and other organics varies significantly at the entrance and exit site of the tunnel, with fluoranthene, pyrene, benzo[a]pyrene, chrysene and benzothiazole having the highest incremented concentrations. The application of Principal Component Analysis and Multiple Linear Regression Analysis helped to identify the emission sources for 82% of the total PM10 mass inside the tunnel. Identified sources include resuspension (27%), diesel exhaust emissions (21%), petrol exhaust emissions (12%), brake wear emissions (11%) and road surface wear (11%). This study shows that major health related chemical species of PM10 originate from non-exhaust sources, further signifying the need for legislation to reduce these emissions.

  15. Ribosomal history reveals origins of modern protein synthesis.

    Directory of Open Access Journals (Sweden)

    Ajith Harish

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

  16. Post-transcriptional regulation of ribosome biogenesis in yeast

    Directory of Open Access Journals (Sweden)

    Isabelle C. Kos-Braun

    2017-05-01

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

  17. Ribosomal Antibiotics: Contemporary Challenges

    Directory of Open Access Journals (Sweden)

    Tamar Auerbach-Nevo

    2016-06-01

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

  18. Effect of primary and secondary radicals on chain breaks in ribosomal RNA in E. coli ribosomes

    International Nuclear Information System (INIS)

    Singh, H.; Bishop, J.

    1984-01-01

    It has been shown previously that, in dilute aerated solutions, ribosomes are inactivated by OH radicals and by secondary radicals produced from added alcohols (Singh and Vadasz 1983 a). In de-aerated solutions, both radicalH and e - sub(aq) also inactivate ribosomes (Singh and Vadasz 1983 b). The results of these studies and other on different systems (Adams et al. 1973, Aldrich and Cundall 1969, Dewey and Stein 1970, Masuda et al. 1971, Nabben et al. 1982, 1983, Samuni et al. 1980, Singh and Singh 1982) have shown that damage to biological systems occurs by diverse mechanisms. One of these mechanisms involves chain breaks in RNA (Pollard and Weller 1967). The purpose of this study was to determine which of the primary and secondary radicals cause chain breaks in ribosomal RNA (rRNA) within the ribosomes. (author)

  19. Towards A Model of Identity and Role Exit

    Directory of Open Access Journals (Sweden)

    Jason S. Milne

    2011-11-01

    Full Text Available Explanations of role exit often focus on how factors associated with a specific role that affect whether the individual will exit a role or not. Other research explains how identities affect our performance in a role. However, no one has yet to demonstrate the connection between role-set factors and identities, and role exit. Using data from a survey of 940 current and former soccer referees, this paper provides a model of role exit that involves a complex of processes that include role-set factors (structural and cultural factors associated with a specific role and identity processes. Specifically, this paper demonstrates that, other than role conflict, identity processes explain the relationship between role-set factors and role exit. The model provides a beginning method for understanding the connection between identities and role exit.

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

    Directory of Open Access Journals (Sweden)

    Francisco J. Espinar-Marchena

    2017-04-01

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

  1. Thermal and Pressure Characterization of a Wind Tunnel Force Balance Using the Single Vector System. Experimental Design and Analysis Approach to Model Pressure and Temperature Effects in Hypersonic Wind Tunnel Research

    Science.gov (United States)

    Lynn, Keith C.; Commo, Sean A.; Johnson, Thomas H.; Parker, Peter A,

    2011-01-01

    Wind tunnel research at NASA Langley Research Center s 31-inch Mach 10 hypersonic facility utilized a 5-component force balance, which provided a pressurized flow-thru capability to the test article. The goal of the research was to determine the interaction effects between the free-stream flow and the exit flow from the reaction control system on the Mars Science Laboratory aeroshell during planetary entry. In the wind tunnel, the balance was exposed to aerodynamic forces and moments, steady-state and transient thermal gradients, and various internal balance cavity pressures. Historically, these effects on force measurement accuracy have not been fully characterized due to limitations in the calibration apparatus. A statistically designed experiment was developed to adequately characterize the behavior of the balance over the expected wind tunnel operating ranges (forces/moments, temperatures, and pressures). The experimental design was based on a Taylor-series expansion in the seven factors for the mathematical models. Model inversion was required to calculate the aerodynamic forces and moments as a function of the strain-gage readings. Details regarding transducer on-board compensation techniques, experimental design development, mathematical modeling, and wind tunnel data reduction are included in this paper.

  2. Active Boundary Layer Control on a Highly Loaded Turbine Exit Case Profile

    Directory of Open Access Journals (Sweden)

    Julia Kurz

    2018-03-01

    Full Text Available A highly loaded turbine exit guide vane with active boundary layer control was investigated experimentally in the High Speed Cascade Wind Tunnel at the University of the German Federal Armed Forces, Munich. The experiments include profile Mach number distributions, wake traverse measurements as well as boundary layer investigations with a flattened Pitot probe. Active boundary layer control by fluidic oscillators was applied to achieve improved performance in the low Reynolds number regime. Low solidity, which can be applied to reduce the number of blades, increases the risk of flow separation resulting in increased total pressure losses. Active boundary layer control is supposed to overcome these negative effects. The experiments show that active boundary layer control by fluidic oscillators is an appropriate way to suppress massive open separation bubbles in the low Reynolds number regime.

  3. Tunnel magnetoresistance in alumina, magnesia and composite tunnel barrier magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Schebaum, Oliver; Drewello, Volker; Auge, Alexander; Reiss, Guenter; Muenzenberg, Markus; Schuhmann, Henning; Seibt, Michael; Thomas, Andy

    2011-01-01

    Using magnetron sputtering, we have prepared Co-Fe-B/tunnel barrier/Co-Fe-B magnetic tunnel junctions with tunnel barriers consisting of alumina, magnesia, and magnesia-alumina bilayer systems. The highest tunnel magnetoresistance ratios we found were 73% for alumina and 323% for magnesia-based tunnel junctions. Additionally, tunnel junctions with a unified layer stack were prepared for the three different barriers. In these systems, the tunnel magnetoresistance ratios at optimum annealing temperatures were found to be 65% for alumina, 173% for magnesia, and 78% for the composite tunnel barriers. The similar tunnel magnetoresistance ratios of the tunnel junctions containing alumina provide evidence that coherent tunneling is suppressed by the alumina layer in the composite tunnel barrier. - Research highlights: → Transport properties of Co-Fe-B/tunnel barrier/Co-Fe-B magnetic tunnel junctions. → Tunnel barrier consists of MgO, Al-Ox, or MgO/Al-Ox bilayer systems. → Limitation of TMR-ratio in composite barrier tunnel junctions to Al-Ox values. → Limitation indicates that Al-Ox layer is causing incoherent tunneling.

  4. Exit or revival?

    International Nuclear Information System (INIS)

    Anon.

    2001-01-01

    The answer given by the international representative at the colloquium:'nuclear: exit or revival? ' was tending towards the revival. The international, democratic, ecological and of energy policy stakes are tackled. (N.C.)

  5. Exit from Synchrony in Joint Improvised Motion.

    Directory of Open Access Journals (Sweden)

    Assi Dahan

    Full Text Available Motion synchrony correlates with effective and well-rated human interaction. However, people do not remain locked in synchrony; Instead, they repeatedly enter and exit synchrony. In many important interactions, such as therapy, marriage and parent-infant communication, it is the ability to exit and then re-enter synchrony that is thought to build strong relationship. The phenomenon of entry into zero-phase synchrony is well-studied experimentally and in terms of mathematical modeling. In contrast, exit-from-synchrony is under-studied. Here, we focus on human motion coordination, and examine the exit-from-synchrony phenomenon using experimental data from the mirror game paradigm, in which people perform joint improvised motion, and from human tracking of computer-generated stimuli. We present a mathematical mechanism that captures aspects of exit-from-synchrony in human motion. The mechanism adds a random motion component when the accumulated velocity error between the players is small. We introduce this mechanism to several models for human coordinated motion, including the widely studied HKB model, and the predictor-corrector model of Noy, Dekel and Alon. In all models, the new mechanism produces realistic simulated behavior when compared to experimental data from the mirror game and from tracking of computer generated stimuli, including repeated entry and exit from zero-phase synchrony that generates a complexity of motion similar to that of human players. We hope that these results can inform future research on exit-from-synchrony, to better understand the dynamics of coordinated action of people and to enhance human-computer and human-robot interaction.

  6. Assessment of exit block following pulmonary vein isolation: far-field capture masquerading as entrance without exit block.

    Science.gov (United States)

    Vijayaraman, Pugazhendhi; Dandamudi, Gopi; Naperkowski, Angela; Oren, Jess; Storm, Randle; Ellenbogen, Kenneth A

    2012-10-01

    Complete electrical isolation of pulmonary veins (PVs) remains the cornerstone of ablation therapy for atrial fibrillation. Entrance block without exit block has been reported to occur in 40% of the patients. Far-field capture (FFC) can occur during pacing from the superior PVs to assess exit block, and this may appear as persistent conduction from PV to left atrium (LA). To facilitate accurate assessment of exit block. Twenty consecutive patients with symptomatic atrial fibrillation referred for ablation were included in the study. Once PV isolation (entrance block) was confirmed, pacing from all the bipoles on the Lasso catheter was used to assess exit block by using a pacing stimulus of 10 mA at 2 ms. Evidence for PV capture without conduction to LA was necessary to prove exit block. If conduction to LA was noticed, pacing output was decreased until there was PV capture without conduction to LA or no PV capture was noted to assess for far-field capture in both the upper PVs. All 20 patients underwent successful isolation (entrance block) of all 76 (4 left common PV) veins: mean age 58 ± 9 years; paroxysmal atrial fibrillation 40%; hypertension 70%, diabetes mellitus 30%, coronary artery disease 15%; left ventricular ejection fraction 55% ± 10%; LA size 42 ± 11 mm. Despite entrance block, exit block was absent in only 16% of the PVs, suggesting persistent PV to LA conduction. FFC of LA appendage was noted in 38% of the left superior PVs. FFC of the superior vena cava was noted in 30% of the right superior PVs. The mean pacing threshold for FFC was 7 ± 4 mA. Decreasing pacing output until only PV capture (loss of FFC) is noted was essential to confirm true exit block. FFC of LA appendage or superior vena cava can masquerade as persistent PV to LA conduction. A careful assessment for PV capture at decreasing pacing output is essential to exclude FFC. Copyright © 2012 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  7. Tritium in Exit Signs | RadTown USA | US EPA

    Science.gov (United States)

    2017-08-07

    Many exit signs contain tritium to light the sign without batteries or electricity. Using tritium in exit signs allows the sign to remain lit if the power goes out. Tritium is most dangerous when it is inhaled or swallowed. Never tamper with a tritium exit sign. If a tritium exit sign is broken, leave the area immediately and notify the building maintenance staff.

  8. Defective ribosome assembly in Shwachman-Diamond syndrome.

    Science.gov (United States)

    Wong, Chi C; Traynor, David; Basse, Nicolas; Kay, Robert R; Warren, Alan J

    2011-10-20

    Shwachman-Diamond syndrome (SDS), a recessive leukemia predisposition disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, skeletal abnormalities and poor growth, is caused by mutations in the highly conserved SBDS gene. Here, we test the hypothesis that defective ribosome biogenesis underlies the pathogenesis of SDS. We create conditional mutants in the essential SBDS ortholog of the ancient eukaryote Dictyostelium discoideum using temperature-sensitive, self-splicing inteins, showing that mutant cells fail to grow at the restrictive temperature because ribosomal subunit joining is markedly impaired. Remarkably, wild type human SBDS complements the growth and ribosome assembly defects in mutant Dictyostelium cells, but disease-associated human SBDS variants are defective. SBDS directly interacts with the GTPase elongation factor-like 1 (EFL1) on nascent 60S subunits in vivo and together they catalyze eviction of the ribosome antiassociation factor eukaryotic initiation factor 6 (eIF6), a prerequisite for the translational activation of ribosomes. Importantly, lymphoblasts from SDS patients harbor a striking defect in ribosomal subunit joining whose magnitude is inversely proportional to the level of SBDS protein. These findings in Dictyostelium and SDS patient cells provide compelling support for the hypothesis that SDS is a ribosomopathy caused by corruption of an essential cytoplasmic step in 60S subunit maturation.

  9. Entry and Exit Dynamics of Nascent Business Owners

    DEFF Research Database (Denmark)

    Rocha, Vera; Carneiro, Anabela; Varum, Celeste

    2015-01-01

    results suggest that different exit modes can be predicted by business owners’ entry route. Furthermore, different exit modes exhibit different duration dependence patterns according to the entry mode. Additionally, the paper shows that businesses started after a displacement episode are not necessarily......This paper reports a comprehensive study on the dynamics of nascent business owners using a unique longitudinal matched employer–employee dataset. We follow over 157,000 individuals who leave paid employment and become business owners during the period 1992–2007. The contributions of this paper...... are twofold. First, we analyze both entry and exit, identifying and characterizing different profiles of individuals leaving paid employment to become business owners, and distinguishing exits by dissolution from exits by ownership transfer. Second, we provide new evidence on how particular experiences...

  10. Modelling the complete operation of a free-piston shock tunnel for a low enthalpy condition

    Science.gov (United States)

    McGilvray, M.; Dann, A. G.; Jacobs, P. A.

    2013-07-01

    Only a limited number of free-stream flow properties can be measured in hypersonic impulse facilities at the nozzle exit. This poses challenges for experimenters when subsequently analysing experimental data obtained from these facilities. Typically in a reflected shock tunnel, a simple analysis that requires small amounts of computational resources is used to calculate quasi-steady gas properties. This simple analysis requires initial fill conditions and experimental measurements in analytical calculations of each major flow process, using forward coupling with minor corrections to include processes that are not directly modeled. However, this simplistic approach leads to an unknown level of discrepancy to the true flow properties. To explore the simple modelling techniques accuracy, this paper details the use of transient one and two-dimensional numerical simulations of a complete facility to obtain more refined free-stream flow properties from a free-piston reflected shock tunnel operating at low-enthalpy conditions. These calculations were verified by comparison to experimental data obtained from the facility. For the condition and facility investigated, the test conditions at nozzle exit produced with the simple modelling technique agree with the time and space averaged results from the complete facility calculations to within the accuracy of the experimental measurements.

  11. Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

    International Nuclear Information System (INIS)

    Guerra-Rebollo, Marta; Mateo, Francesca; Franke, Kristin; Huen, Michael S.Y.; Lopitz-Otsoa, Fernando; Rodríguez, Manuel S.; Plans, Vanessa; Thomson, Timothy M.

    2012-01-01

    The induction of DNA double-strand breaks (DSBs) elicits a plethora of responses that redirect many cellular functions to the vital task of repairing the injury, collectively known as the DNA damage response (DDR). We have found that, in the absence of DNA damage, the DSB repair factors RNF8 and BRCA1 are associated with the nucleolus. Shortly after exposure of cells to γ-radiation, RNF8 and BRCA1 translocated from the nucleolus to damage foci, a traffic that was reverted several hours after the damage. RNF8 interacted through its FHA domain with the ribosomal protein RPSA, and knockdown of RPSA caused a depletion of nucleolar RNF8 and BRCA1, suggesting that the interaction of RNF8 with RPSA is critical for the nucleolar localization of these DDR factors. Knockdown of RPSA or RNF8 impaired bulk protein translation, as did γ-irradiation, the latter being partially countered by overexpression of exogenous RNF8. Our results suggest that RNF8 and BRCA1 are anchored to the nucleolus through reversible interactions with RPSA and that, in addition to its known functions in DDR, RNF8 may play a role in protein synthesis, possibly linking the nucleolar exit of this factor to the attenuation of protein synthesis in response to DNA damage. -- Highlights: ► RNF8 and BRCA1 are associated with the nucleolus of undamaged cells. ► Upon γ-radiation, RNF8 and BRCA1 are translocated from the nucleolus to damage foci. ► The ribosomal protein RPSA anchors RNF8 to the nucleolus. ► RNF8 may play previously unsuspected roles in protein synthesis.

  12. Emerging functions of ribosomal proteins in gene-specific transcription and translation

    International Nuclear Information System (INIS)

    Lindstroem, Mikael S.

    2009-01-01

    Ribosomal proteins have remained highly conserved during evolution presumably reflecting often critical functions in ribosome biogenesis or mature ribosome function. In addition, several ribosomal proteins possess distinct extra-ribosomal functions in apoptosis, DNA repair and transcription. An increasing number of ribosomal proteins have been shown to modulate the trans-activation function of important regulatory proteins such as NF-κB, p53, c-Myc and nuclear receptors. Furthermore, a subset of ribosomal proteins can bind directly to untranslated regions of mRNA resulting in transcript-specific translational control outside of the ribosome itself. Collectively, these findings suggest that ribosomal proteins may have a wider functional repertoire within the cell than previously thought. The future challenge is to identify and validate these novel functions in the background of an often essential primary function in ribosome biogenesis and cell growth.

  13. Exploring the Reasons and Ways to Exit: The Entrepreneur Perspective

    NARCIS (Netherlands)

    Parastuty, Zulaicha; Breitenecker, Robert J.; Schwarz, Erich J.; Harms, Rainer; Bögenhold, Dieter; Bonnet, Jean; Dejardin, Marcus; Garcia Perez de Lema, Domingo

    2016-01-01

    Research on entrepreneurial exit has received growing attention recently, attributing to the importance of exit in the entrepreneurial process. Yet, the complex phenomena of exit render the research scattered in the field. This research is aimed at understanding entrepreneurial exit at the

  14. The Political Economy of Early Exit

    DEFF Research Database (Denmark)

    Schmitt, Carina; Starke, Peter

    2016-01-01

    Large-scale exit from the labour market began in the 1970s in many OECD countries. The literature indicates that individual early retirement decisions are facilitated by generous and accessible ‘pathways’ into retirement in the public pension system, unemployment insurance or disability benefits....... in the tradable sector, against a more traditional class-based logic of welfare state policy-making. Quantitative analysis of employment outcomes in 21 countries shows that the political economy of early exit clearly rests on the sectoral politics of cost-shifting.......Large-scale exit from the labour market began in the 1970s in many OECD countries. The literature indicates that individual early retirement decisions are facilitated by generous and accessible ‘pathways’ into retirement in the public pension system, unemployment insurance or disability benefits....... It is unclear, however, why early exit became so much more prevalent in some countries than in others and why such differences remain, despite a recent shift back towards higher employment rates and ‘active ageing’. We test a logic of sectoral cost-shifting politics involving cross-class alliances...

  15. The Beginner's Guide to Wind Tunnels with TunnelSim and TunnelSys

    Science.gov (United States)

    Benson, Thomas J.; Galica, Carol A.; Vila, Anthony J.

    2010-01-01

    The Beginner's Guide to Wind Tunnels is a Web-based, on-line textbook that explains and demonstrates the history, physics, and mathematics involved with wind tunnels and wind tunnel testing. The Web site contains several interactive computer programs to demonstrate scientific principles. TunnelSim is an interactive, educational computer program that demonstrates basic wind tunnel design and operation. TunnelSim is a Java (Sun Microsystems Inc.) applet that solves the continuity and Bernoulli equations to determine the velocity and pressure throughout a tunnel design. TunnelSys is a group of Java applications that mimic wind tunnel testing techniques. Using TunnelSys, a team of students designs, tests, and post-processes the data for a virtual, low speed, and aircraft wing.

  16. Eukaryotic ribosome display with in situ DNA recovery.

    Science.gov (United States)

    He, Mingyue; Edwards, Bryan M; Kastelic, Damjana; Taussig, Michael J

    2012-01-01

    Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and eukaryotic ribosome display systems have been developed. In this chapter, we describe the eukaryotic rabbit reticulocyte method in which a distinct in situ single-primer RT-PCR procedure is used to recover DNA from the selected PRM complexes without the need for prior disruption of the ribosome.

  17. 29 CFR 1910.36 - Design and construction requirements for exit routes.

    Science.gov (United States)

    2010-07-01

    ... construction requirements for exit routes. (a) Basic requirements. Exit routes must meet the following design... your workplace, consult NFPA 101-2000, Life Safety Code. (c) Exit discharge. (1) Each exit discharge... route must be adequate. (1) Exit routes must support the maximum permitted occupant load for each floor...

  18. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.

    Science.gov (United States)

    Shi, Zhen; Fujii, Kotaro; Kovary, Kyle M; Genuth, Naomi R; Röst, Hannes L; Teruel, Mary N; Barna, Maria

    2017-07-06

    Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) exists and enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with differential selectivity for translating subpools of transcripts, including those controlling metabolism, cell cycle, and development. As an example, mRNAs enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their efficient translation. Within several of these transcripts, this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Effect of sodium fluoride on the amount of polyribosomes, single ribosomes and ribosomal subunits in a cellular slime mold, Dictyostelium discoideum

    Energy Technology Data Exchange (ETDEWEB)

    Sameshima, M; Ito, K; Iwabuchi, M

    1972-01-01

    In the slime mold, Dictyostelium discoideum, when the rate of protein synthesis was decreased by NaF, free 80-S ribosomes accumulated at the expense of polyribosomes, while 60-S and 40-S ribosomal subunits remained almost constant. The same level of ribosomal subunits was also maintained in cells after incubation with cycloheximide or at the stationary phase of growth.

  20. Spatial signals link exit from mitosis to spindle position.

    Science.gov (United States)

    Falk, Jill Elaine; Tsuchiya, Dai; Verdaasdonk, Jolien; Lacefield, Soni; Bloom, Kerry; Amon, Angelika

    2016-05-11

    In budding yeast, if the spindle becomes mispositioned, cells prevent exit from mitosis by inhibiting the mitotic exit network (MEN). The MEN is a signaling cascade that localizes to spindle pole bodies (SPBs) and activates the phosphatase Cdc14. There are two competing models that explain MEN regulation by spindle position. In the 'zone model', exit from mitosis occurs when a MEN-bearing SPB enters the bud. The 'cMT-bud neck model' posits that cytoplasmic microtubule (cMT)-bud neck interactions prevent MEN activity. Here we find that 1) eliminating cMT- bud neck interactions does not trigger exit from mitosis and 2) loss of these interactions does not precede Cdc14 activation. Furthermore, using binucleate cells, we show that exit from mitosis occurs when one SPB enters the bud despite the presence of a mispositioned spindle. We conclude that exit from mitosis is triggered by a correctly positioned spindle rather than inhibited by improper spindle position.

  1. 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.

  2. The Phosphorylation of Ribosomal Protein in Lemna minor

    Science.gov (United States)

    Trewavas, A.

    1973-01-01

    Sterile cultures of Lemna minor have been labeled with 32P1, and the ribosomal proteins have been examined for radioactivity. In relatively short term labeling a radioactive protein was found which ran as a single component in both urea/acetic acid and sodium lauryl sulfate gel electrophoresis. Acid hydrolysis of the labeled protein permitted the isolation of serine phosphate. After labeling to equilibrium with 32P1, calculation indicated only 0.6 to 0.75 atom of this protein phosphorus per ribosome. The phosphorylated protein is found in both polysomes and “derived” monomers and appears to be located in the ribosomal small subunit. Its apparent molecular weight is 42,000. Addition of growth-inhibiting concentrations of abscisic acid does not alter the apparent degree of labeling of this protein in 5 hours, but after 24 hours of treatment the total protein phosphorus was reduced from 0.75 atom of phosphorus per ribosome to 0.36 atom of phosphorus per ribosome. PMID:16658405

  3. Dissuasive exit signage for building fire evacuation.

    Science.gov (United States)

    Olander, Joakim; Ronchi, Enrico; Lovreglio, Ruggiero; Nilsson, Daniel

    2017-03-01

    This work presents the result of a questionnaire study which investigates the design of dissuasive emergency signage, i.e. signage conveying a message of not utilizing a specific exit door. The work analyses and tests a set of key features of dissuasive emergency signage using the Theory of Affordances. The variables having the largest impact on observer preference, interpretation and noticeability of the signage have been identified. Results show that features which clearly negate the exit-message of the original positive exit signage are most effective, for instance a red X-marking placed across the entirety of the exit signage conveys a clear dissuasive message. Other features of note are red flashing lights and alternation of colour. The sense of urgency conveyed by the sign is largely affected by sensory inputs such as red flashing lights or other features which cause the signs to break the tendencies of normalcy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.

    Directory of Open Access Journals (Sweden)

    Brittany Burton

    Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.

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

    DEFF Research Database (Denmark)

    Issinger, O G

    1977-01-01

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

  6. Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Guerra-Rebollo, Marta; Mateo, Francesca; Franke, Kristin [Department of Cell Biology, Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona (Spain); Huen, Michael S.Y. [Department of Anatomy, Centre for Cancer Research, The University of Hong Kong, L1, Laboratory Block, 21 Sassoon Road, Hong Kong Special Administrative Region (Hong Kong); Lopitz-Otsoa, Fernando; Rodriguez, Manuel S. [Proteomics Unit, CIC bioGUNE CIBERehd, ProteoRed, Technology Park of Bizkaia, Building 801A, 48160 Derio (Spain); Plans, Vanessa [Department of Cell Biology, Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona (Spain); Thomson, Timothy M., E-mail: titbmc@ibmb.csic.es [Department of Cell Biology, Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona (Spain)

    2012-11-01

    The induction of DNA double-strand breaks (DSBs) elicits a plethora of responses that redirect many cellular functions to the vital task of repairing the injury, collectively known as the DNA damage response (DDR). We have found that, in the absence of DNA damage, the DSB repair factors RNF8 and BRCA1 are associated with the nucleolus. Shortly after exposure of cells to {gamma}-radiation, RNF8 and BRCA1 translocated from the nucleolus to damage foci, a traffic that was reverted several hours after the damage. RNF8 interacted through its FHA domain with the ribosomal protein RPSA, and knockdown of RPSA caused a depletion of nucleolar RNF8 and BRCA1, suggesting that the interaction of RNF8 with RPSA is critical for the nucleolar localization of these DDR factors. Knockdown of RPSA or RNF8 impaired bulk protein translation, as did {gamma}-irradiation, the latter being partially countered by overexpression of exogenous RNF8. Our results suggest that RNF8 and BRCA1 are anchored to the nucleolus through reversible interactions with RPSA and that, in addition to its known functions in DDR, RNF8 may play a role in protein synthesis, possibly linking the nucleolar exit of this factor to the attenuation of protein synthesis in response to DNA damage. -- Highlights: Black-Right-Pointing-Pointer RNF8 and BRCA1 are associated with the nucleolus of undamaged cells. Black-Right-Pointing-Pointer Upon {gamma}-radiation, RNF8 and BRCA1 are translocated from the nucleolus to damage foci. Black-Right-Pointing-Pointer The ribosomal protein RPSA anchors RNF8 to the nucleolus. Black-Right-Pointing-Pointer RNF8 may play previously unsuspected roles in protein synthesis.

  7. On the control of ribosomal protein biosynthesis in Escherichia coli

    International Nuclear Information System (INIS)

    Pichon, J.; Marvaldi, J.; Coeroli, C.; Cozzone, A.; Marchis-Mouren, G.

    1977-01-01

    The rate of individual ribosomal protein synthesis relative to total protein synthesis has been determined in Escherichia coli rel + and rel - cells, under valyl-tRNA deprivation. These strains have a temperature-sensitive valyl-tRNA synthetase. Starvation was obtained following transfer of the cells to non-permissive temperature. Ribosomal proteins were obtained by treatment of either total lysates of freeze-thawed lysozyme spheroplasts or ammonium sulphate precipitate of ribosomes, with acetic acid. Differential labelling of the ribosomal proteins was observed in both strains: proteins from the rel + strain appear more labelled than those from the rel - strain, the rate of labelling of individual proteins being about the same in both strains. Moreover ribosomal proteins were found as stable during starvation as total protein. It is thus concluded that in starving cells individual ribosomal proteins are not synthesized at equal rates. This indicates that the synthesis of ribosomal proteins is not only under the control of the rel gene

  8. Exit interviews to reduce turnover amongst healthcare professionals.

    Science.gov (United States)

    Webster, Joan; Flint, Anndrea

    2014-08-19

    Exit interviews are widely used in healthcare organisations to identify reasons for staff attrition, yet their usefulness in limiting turnover is unclear. To determine the effectiveness of various exit interview strategies in decreasing turnover rates amongst healthcare professionals. We searched the Cochrane EPOC Group Specialised Register; Cochrane Central Register of Controlled Trials (CENTRAL), Issue 11, 2012; MEDLINE, Ovid (1950- ); EMBASE, Ovid (1947- ); CINAHL, EbscoHost (1980- ), and PsycINFO, OVID (1806-) between October 31 and November 6, 2012. We also screened the reference lists of included studies and relevant reviews; and searched trial registries for planned and on-going studies. We did not restrict searches by language or publication date. Randomised controlled trials, controlled clinical trials, controlled before-after studies and interrupted time series studies comparing turnover rates between healthcare professionals who had undergone one form of exit interview with another form of exit interview or with no interview. Two review authors independently assessed trial quality and extracted data. The original search identified 1560 citations, of which we considered 19 potentially relevant. The two authors independently reviewed the abstracts of these studies and retrieved the full texts of eight studies. We excluded all eight following independent assessment; they were either interviews, commentaries on how to do an exit interview or descriptive studies about reasons for leaving. We found no studies that matched our inclusion criteria. For this first update, we screened 2220 citations and identified no new studies. Evidence about the effectiveness of exit interviews to reduce turnover is currently not available. However, exit interviews may provide useful information about the work environment which, in turn, may be useful in the development of interventions to reduce turnover.

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

    NARCIS (Netherlands)

    Essers, P.B.M.

    2013-01-01

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

  10. The primary structures of ribosomal proteins S14 and S16 from the archaebacterium Halobacterium marismortui. Comparison with eubacterial and eukaryotic ribosomal proteins.

    Science.gov (United States)

    Kimura, J; Kimura, M

    1987-09-05

    The amino acid sequences of two ribosomal proteins, S14 and S16, from the archaebacterium Halobacterium marismortui have been determined. Sequence data were obtained by the manual and solid-phase sequencing of peptides derived from enzymatic digestions with trypsin, chymotrypsin, pepsin, and Staphylococcus aureus protease as well as by chemical cleavage with cyanogen bromide. Proteins S14 and S16 contain 109 and 126 amino acid residues and have Mr values of 11,964 and 13,515, respectively. Comparison of the sequences with those of ribosomal proteins from other organisms demonstrates that S14 has a significant homology with the rat liver ribosomal protein S11 (36% identity) as well as with the Escherichia coli ribosomal protein S17 (37%), and that S16 is related to the yeast ribosomal protein YS22 (40%) and proteins S8 from E. coli (28%) and Bacillus stearothermophilus (30%). A comparison of the amino acid residues in the homologous regions of halophilic and nonhalophilic ribosomal proteins reveals that halophilic proteins have more glutamic acids, asparatic acids, prolines, and alanines, and less lysines, arginines, and isoleucines than their nonhalophilic counterparts. These amino acid substitutions probably contribute to the structural stability of halophilic ribosomal proteins.

  11. Exit examinations, peer academic climate, and adolescents' developmental outcomes.

    Science.gov (United States)

    Benner, Aprile D

    2013-02-01

    Implications of high school exit examination performance were examined with a sample of 672 racial/ethnic minority students. Exit examination failure in the 10th grade was negatively linked to subsequent grade point average, school engagement, and school belonging one year later, controlling for outcomes prior to taking the examination. Academically incongruent students-those who failed the exit examination but were in schools where their same-race/ethnicity peers were performing well academically-seemed to be at particular risk for struggling grades and poorer socioemotional well-being (e.g., experiencing greater depressive symptoms and loneliness). Findings contribute to the limited research base on exit examinations and highlight the links between exit examination performance and developmental outcomes beyond the oft-studied academic domain. Copyright © 2012 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  12. Acoustic Radiation from High-Speed Turbulent Boundary Layers in a Tunnel-Like Environment

    Science.gov (United States)

    Duan, Lian; Choudhari, Meelan M.; Zhang, Chao

    2015-01-01

    Direct numerical simulation of acoustic radiation from a turbulent boundary layer in a cylindrical domain will be conducted under the flow conditions corresponding to those at the nozzle exit of the Boeing/AFOSR Mach-6 Quiet Tunnel (BAM6QT) operated under noisy-flow conditions with a total pressure p(sub t) of 225 kPa and a total temperature of T(sub t) equal to 430 K. Simulations of acoustic radiation from a turbulent boundary layer over a flat surface are used as a reference configuration to illustrate the effects of the cylindrical enclosure. A detailed analysis of acoustic freestream disturbances in the cylindrical domain will be reported in the final paper along with a discussion pertaining to the significance of the flat-plate acoustic simulations and guidelines concerning the modeling of the effects of an axisymmetric tunnel wall on the noise field.

  13. Hypoxic stress-induced changes in ribosomes of maize seedling roots

    International Nuclear Information System (INIS)

    Bailey-Serres, J.; Freeling, M.

    1990-01-01

    The hypoxic stress response of Zea mays L. seedling roots involves regulation of gene expression at transcriptional and posttranscriptional levels. We investigated the effect of hypoxia on the translational machinery of seedling roots. The levels of monoribosomes and ribosomal subunits increased dramatically within 1 hour of stress. Prolonged hypoxia resulted in continued accumulation of nontranslating ribosomes, as well as increased levels of small polyribosomes. The return of seedlings to normal aerobic conditions resulted in recovery of normal polyribosome levels. Comparison of ribosomal proteins from control and hypoxic roots revealed differences in quantity and electrophoretic mobility. In vivo labeling of roots with [ 35 S]methionine revealed variations in newly synthesized ribosomal proteins. In vivo labeling of roots with [ 32 P]orthophosphate revealed a major reduction in the phosphorylation of a 31 kilodalton ribosomal protein in hypoxic stressed roots. In vitro phosphorylation of ribosomal proteins by endogenous kinases was used to probe for differences in ribosome structure and composition. The patterns of in vitro kinased phosphoproteins of ribosomes from control and hypoxic roots were not identical. Variation in phosphoproteins of polyribosomes from control and hypoxic roots, as well as among polyribosomes from hypoxic roots were observed. These results indicate that modification of the translational machinery occurs in response to hypoxic stress

  14. Ribosomes slide on lysine-encoding homopolymeric A stretches

    Science.gov (United States)

    Koutmou, Kristin S; Schuller, Anthony P; Brunelle, Julie L; Radhakrishnan, Aditya; Djuranovic, Sergej; Green, Rachel

    2015-01-01

    Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell-free expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome ‘sliding’ represents an unexpected type of ribosome movement possible during translation. DOI: http://dx.doi.org/10.7554/eLife.05534.001 PMID:25695637

  15. The Unexplored Mechanisms and Regulatory Functions of Ribosomal Translocation

    Science.gov (United States)

    Alejo, Jose Luis

    In every cell, protein synthesis is carried out by the ribosome, a complex macromolecular RNA-protein assembly. Decades of structural and kinetic studies have increased our understanding of ribosome initiation, decoding, translocation and termination. Yet, the underlying mechanism of these fundamental processes has yet to be fully delineated. Hence, the molecular basis of regulation remains obscure. Here, single-molecule fluorescence methods are applied to decipher the mechanism and regulatory roles of the multi-step process of directional substrate translocation on the ribosome that accompanies every round of protein synthesis. In Chapter 1, single-molecule fluorescence resonance energy transfer (smFRET) is introduced as a tool for studying bacterial ribosome translocation. Chapter 2 details the experimental methods. In Chapter 3, the elongation factor G(EF-G)-catalyzed movement of substrates through the ribosome is examined from several perspectives or signals reporting on various degrees of freedom of ribosome dynamics. Two ribosomal states interconvert in the presence of EF-G(GDP), displaying novel head domain motions, until relocking takes place. In Chapter 4, in order to test if the mentioned fluctuations leading to relocking are correlated to the engagement of the P-site by the peptidyl-tRNA, the translocation of miscoded tRNAs is studied. Severe defects in the relocking stages of translocation reveal the correlation between this new stage of translocation and P-site tRNA engagement.

  16. Is the publication of exit poll results morally permissible?

    DEFF Research Database (Denmark)

    Sønderholm, Jørn

    2016-01-01

    This article is about exit polls. It addresses the question of whether or not it is morally permissible to publish exit poll results. The conclusion of the article is that an affirmative answer should be given to this question. In section 2, the master argument in favor of the moral permissibility...... of the publication of exit poll results is introduced. This is a strong argument. It is, however, argued that it might be the case that the conclusion of this argument should be rejected if there are other, and weightier, arguments against the idea that the publication of exit poll results is morally permissible....... In section 3, the strongest arguments against the moral permissibility of the publication of exit poll results are outlined and discussed. The conclusion of this section is that all these arguments fail in their intended purpose. The conclusion of the article is therefore justified....

  17. IPO as an Exit startegy in Management Buyouts

    OpenAIRE

    Sheth, Vidhi Chetan

    2008-01-01

    The basic subject to this research project is,IPO as an exit strategy in management buyouts. The paper provides with an understanding of the various characteristics and factors that have an impact on a buyout exit through an IPO. Discussions on the issues like the IPO versus other exit strategies, performance of a company's pre-IPO as well as post-IPO, the trends in the buyout and the IPO market, etc are done. For a better understanding and an in-depth knowledge about the topic, we have analy...

  18. Exit by Afghanisation

    DEFF Research Database (Denmark)

    Holmberg, Hasse

    USA’s exit-strategi fra Afghanistan har båret præg af et italesat hovedmål om overdragelse af ansvar til de nationale myndigheder i landet. Exit-strategien udmærker sig ved sin lighed med USA’s afvikling af sit engagement i Vietnam for snart et halvt århundrede siden, hvor begrebet Vietnamisation...... om national selvbestemmelse. Den amerikanske opinion spillede en afgørende rolle og afslutningen af engagementet i Vietnam kan i lige så høj grad ses som en reaktion på den massive folkelige modstand mod krigen. Omtrent 40 år efter kan Obama-administrationen notere sig en lignende negativ trend i...... Kissinger vidste, at krigen i Vietnam var tabt. Vietnamisation havde i høj grad til formål at slutte USA’s engagement på en måde, der tog hensyn til USA’s internationale renomme. Spørgsmålet er så om de mange strategiske ligheder kan overføres til samme konklusion: krigen er tabt. Briefet har til hensigt...

  19. Entry and exit decisions under uncertainty

    DEFF Research Database (Denmark)

    Kongsted, Hans Christian

    1996-01-01

    This paper establishes the general deterministic limit that corresponds to Dixit's model of entry and exit decisions under uncertainty. The interlinked nature of decisions is shown to be essential also in the deterministic limit. A numerical example illustrates the result......This paper establishes the general deterministic limit that corresponds to Dixit's model of entry and exit decisions under uncertainty. The interlinked nature of decisions is shown to be essential also in the deterministic limit. A numerical example illustrates the result...

  20. Tunneling technologies for the collider ring tunnels

    International Nuclear Information System (INIS)

    Frobenius, P.

    1989-01-01

    The Texas site chosen for the Superconducting Super Collider has been studied, and it has been determined that proven, conventional technology and accepted engineering practice are suitable for constructing the collider tunnels. The Texas National Research Laboratory Commission report recommended that two types of tunneling machines be used for construction of the tunnels: a conventional hard rock tunnel boring machine (TBM) for the Austin chalk and a double shielded, rotary TBM for the Taylor marl. Since the tunneling machines usually set the pace for the project, efficient planning, operation, and coordination of the tunneling system components will be critical to the schedule and cost of the project. During design, tunneling rate prediction should be refined by focusing on the development of an effective tunneling system and evaluating its capacity to meet or exceed the required schedules. 8 refs., 13 figs

  1. Unstable structure of ribosomal particles synthesized in. gamma. -irradiated Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Fujita, H; Morita, K [National Inst. of Radiological Sciences, Chiba (Japan)

    1975-06-01

    Stability of Escherichia coli ribosomes newly synthesized after ..gamma..-irradiation was compared with that of normal ribosomes. The ribosomal particles around 70-S synthesized in irradiated cells were more sensitive to digestion by pancreatic ribonuclease A. A larger number of the salt-unstable '50-S' precursor particles existed in the extract from irradiated cells than in the extract from unirradiated cells. These facts suggest that ribosomal particles, synthesized during an earlier stage in irradiated cells, maintain an incomplete structure even though they are not distinguishable from normal ribosomes by means of sucrose density-gradient centrifugation.

  2. Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research.

    Science.gov (United States)

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

    2017-01-01

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

  3. A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly

    International Nuclear Information System (INIS)

    Lott, Brittany Burton; Wang, Yongmei; Nakazato, Takuya

    2013-01-01

    Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960’s, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear. We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. We compared small subunit (30S) r-protein sequences to those of other housekeeping proteins from 560 bacterial species and searched for correlations between r-protein amino acid content and factors such as assembly binding order, environmental growth temperature, protein size, and contact with ribosomal RNA (rRNA) in the 30S complex. We find r-proteins have a significantly high percent of positive residues, which are highly represented at rRNA contact sites. An inverse correlation between the percent of positive residues and r-protein size was identified and is mainly due to the content of Lysine residues, rather than Arginine. Nearly all r-proteins carry a net positive charge, but no statistical correlation between the net charge and the binding order was detected. Thermophilic (high-temperature) r-proteins contain increased Arginine, Isoleucine, and Tyrosine, and decreased Serine and Threonine compared to mesophilic (lower-temperature), reflecting a known distinction between thermophiles and mesophiles, possibly to account for protein thermostability. However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different. Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction. However, the binding order of

  4. Hierarchical recruitment of ribosomal proteins and assembly factors remodels nucleolar pre-60S ribosomes.

    Science.gov (United States)

    Biedka, Stephanie; Micic, Jelena; Wilson, Daniel; Brown, Hailey; Diorio-Toth, Luke; Woolford, John L

    2018-04-24

    Ribosome biogenesis involves numerous preribosomal RNA (pre-rRNA) processing events to remove internal and external transcribed spacer sequences, ultimately yielding three mature rRNAs. Removal of the internal transcribed spacer 2 spacer RNA is the final step in large subunit pre-rRNA processing and begins with endonucleolytic cleavage at the C 2 site of 27SB pre-rRNA. C 2 cleavage requires the hierarchical recruitment of 11 ribosomal proteins and 14 ribosome assembly factors. However, the function of these proteins in C 2 cleavage remained unclear. In this study, we have performed a detailed analysis of the effects of depleting proteins required for C 2 cleavage and interpreted these results using cryo-electron microscopy structures of assembling 60S subunits. This work revealed that these proteins are required for remodeling of several neighborhoods, including two major functional centers of the 60S subunit, suggesting that these remodeling events form a checkpoint leading to C 2 cleavage. Interestingly, when C 2 cleavage is directly blocked by depleting or inactivating the C 2 endonuclease, assembly progresses through all other subsequent steps. © 2018 Biedka et al.

  5. gamma. radiation effect on the functional properties of the cotton ribosomes

    Energy Technology Data Exchange (ETDEWEB)

    Ibragimov, A P; Safarov, Sh

    1973-01-01

    A study is made of the action of radiation on the functional properties of ribosomes in irradiated organisms and on isolated ribosomes exposed to different doses. With increase in dose there occurs a reduction in the incorporation of labelled amino acids by the ribosomes released from irradiated sprouts and also during irradiation of isolated ribosomes. The study covered the functional activity of ribosomes irradiated at different doses with the use of synthetic poly-U and poly-A matrices synthesizing polyphenylalanine and polylysine, depending on the irradiation dose. The inhibition of the activity of the protein synthesis system at high doses is due to structural and functional changes in ribosomes and also to disturbance in the biosynthesis and functions of the messenger RNA.

  6. Criticality safety analysis of a calciner exit chute

    International Nuclear Information System (INIS)

    Haught, C.F.; Basoglu, B.; Brewer, R.W.; Hollenback, D.F.; Wilkinson, A.D.; Dodds, H.L.

    1994-01-01

    Calcination of uranyl nitrate into uranium oxide is part of normal operations of some enrichment plants. Typically, a calciner discharges uranium oxide powder (U 3 O 8 ) into an exit chute that directs the powder into a receiving can located in a glove box. One possible scenario for a criticality accident is the exit chute becoming blocked with powder near its discharge. The blockage restricts the flow of powder causing the exit chute to become filled with the powder. If blockage does occur, the height of the powder could reach a level that would not be safe from a criticality point of view. In this analysis, the subcritical height limit is examined for 98% enriched U 3 O 8 in the exit chute with full water reflection and optimal water moderation. The height limit for ensuring criticality safety during such an accumulation is 28.2 cm above the top of the discharge pipe at the bottom of the chute. Chute design variations are also evaluated with full water reflection and optimal water moderation. Subcritical configurations for the exit chute variation are developed, but the configurations are not safe when combined with the calciner. To ensure criticality safety, modifications must be made to the calciner tube or safety measures must be implemented if these designs are to be utilized with 98% enriched material. A geometrically safe configuration for the exit chute is developed for a blockage of 20% enriched powder with full water reflection and optimal water moderation, and this configuration is safe when combined with the existing calciner

  7. Interaction of tRNA with Eukaryotic Ribosome

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer

    2015-03-01

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

  8. Macrolide antibiotic interaction and resistance on the bacterial ribosome.

    Science.gov (United States)

    Poehlsgaard, Jacob; Douthwaite, Stephen

    2003-02-01

    Our understanding of the fine structure of many antibiotic target sites has reached a new level of enlightenment in the last couple of years due to the advent, by X-ray crystallography, of high-resolution structures of the bacterial ribosome. Many classes of clinically useful antibiotics bind to the ribosome to inhibit bacterial protein synthesis. Macrolide, lincosamide and streptogramin B (MLSB) antibiotics form one of the largest groups, and bind to the same site on the 50S ribosomal subunit. Here, we review the molecular details of the ribosomal MLSB site to put into perspective the main points from a wealth of biochemical and genetic data that have been collected over several decades. The information is now available to understand, at atomic resolution, how macrolide antibiotics interact with their ribosomal target, how the target is altered to confer resistance, and in which directions we need to look if we are to rationally design better drugs to overcome the extant resistance mechanisms.

  9. Cis-regulatory RNA elements that regulate specialized ribosome activity.

    Science.gov (United States)

    Xue, Shifeng; Barna, Maria

    2015-01-01

    Recent evidence has shown that the ribosome itself can play a highly regulatory role in the specialized translation of specific subpools of mRNAs, in particular at the level of ribosomal proteins (RP). However, the mechanism(s) by which this selection takes place has remained poorly understood. In our recent study, we discovered a combination of unique RNA elements in the 5'UTRs of mRNAs that allows for such control by the ribosome. These mRNAs contain a Translation Inhibitory Element (TIE) that inhibits general cap-dependent translation, and an Internal Ribosome Entry Site (IRES) that relies on a specific RP for activation. The unique combination of an inhibitor of general translation and an activator of specialized translation is key to ribosome-mediated control of gene expression. Here we discuss how these RNA regulatory elements provide a new level of control to protein expression and their implications for gene expression, organismal development and evolution.

  10. Yeast ribosomal proteins

    International Nuclear Information System (INIS)

    Otaka, E.; Kobata, K.

    1978-01-01

    The cytoplasmic 80s ribosomal proteins from the cells of yeast Saccharomyces cerevisiae were analyzed by SDS two-dimensional polyacrylamide gel electrophoresis. Seventyfour proteins were identified and consecutively numbered from 1 to 74. Upon oxidation of the 80s proteins with performic acid, ten proteins (no. 15, 20, 35, 40, 44, 46, 49, 51, 54 and 55) were dislocated on the gel without change of the total number of protein spots. Five proteins (no. 8, 14, 16, 36 and 74) were phosphorylated in vivo as seen in 32 P-labelling experiments. The large and small subunits separated in low magnesium medium were analyzed by the above gel electrophoresis. At least forty-five and twenty-eight proteins were assumed to be in the large and small subunits, respectively. All proteins found in the 80s ribosomes, except for no. 3, were detected in either subunit without appearance of new spots. The acidic protein no. 3 seems to be lost during subunit dissociation. (orig.) [de

  11. 24 CFR 3280.106 - Exit facilities; egress windows and devices.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Exit facilities; egress windows and... § 3280.106 Exit facilities; egress windows and devices. (a) Every room designed expressly for sleeping purposes, unless it has an exit door (see § 3280.105), shall have at least one outside window or approved...

  12. An Identity Theory of Role Exit among Soccer Referees

    OpenAIRE

    Milne, Jason Syme

    2006-01-01

    This study examines how identity processes affect role exit. I test a model of role exit that situates the identity processes of cognitive processes (reflected appraisals and social comparisons), rewards and costs related to the role, commitment to the role, and identity centrality as mediating factors between role-set and social characteristic background factors, and role exit. Using a sample of 940 current and former soccer referees in Virginia and the District of Columbia, the results s...

  13. Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis

    Science.gov (United States)

    Onouchi, Hitoshi; Nagami, Yoko; Haraguchi, Yuhi; Nakamoto, Mari; Nishimura, Yoshiko; Sakurai, Ryoko; Nagao, Nobuhiro; Kawasaki, Daisuke; Kadokura, Yoshitomo; Naito, Satoshi

    2005-01-01

    Expression of the Arabidopsis CGS1 gene that codes for cystathionine γ-synthase is feedback regulated at the step of mRNA stability in response to S-adenosyl-L-methionine (AdoMet). A short stretch of amino acid sequence, called the MTO1 region, encoded by the first exon of CGS1 itself is involved in this regulation. Here, we demonstrate, using a cell-free system, that AdoMet induces temporal translation elongation arrest at the Ser-94 codon located immediately downstream of the MTO1 region, by analyzing a translation intermediate and performing primer extension inhibition (toeprint) analysis. This translation arrest precedes the formation of a degradation intermediate of CGS1 mRNA, which has its 5′ end points near the 5′ edge of the stalled ribosome. The position of ribosome stalling also suggests that the MTO1 region in nascent peptide resides in the ribosomal exit tunnel when translation elongation is temporarily arrested. In addition to the MTO1 region amino acid sequence, downstream Trp-93 is also important for the AdoMet-induced translation arrest. This is the first example of nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in eukaryotes. Furthermore, our data suggest that the ribosome stalls at the step of translocation rather than at the step of peptidyl transfer. PMID:16027170

  14. Trapping the ribosome to control gene expression.

    Science.gov (United States)

    Boehringer, Daniel; Ban, Nenad

    2007-09-21

    Protein synthesis is often regulated by structured mRNAs that interact with ribosomes. In this issue of Cell, Marzi et al. (2007) provide insights into the autoregulation of protein S15 by visualizing the folded repressor mRNA on the ribosome stalled in the preinitiation state. These results have implications for our understanding of the mechanism of translation initiation in general.

  15. A Listeria monocytogenes RNA helicase essential for growth and ribosomal maturation at low temperatures uses its C terminus for appropriate interaction with the ribosome.

    Science.gov (United States)

    Netterling, Sakura; Vaitkevicius, Karolis; Nord, Stefan; Johansson, Jörgen

    2012-08-01

    Listeria monocytogenes, a Gram-positive food-borne human pathogen, is able to grow at temperatures close to 0°C and is thus of great concern for the food industry. In this work, we investigated the physiological role of one DExD-box RNA helicase in Listeria monocytogenes. The RNA helicase Lmo1722 was required for optimal growth at low temperatures, whereas it was dispensable at 37°C. A Δlmo1722 strain was less motile due to downregulation of the major subunit of the flagellum, FlaA, caused by decreased flaA expression. By ribosomal fractionation experiments, it was observed that Lmo1722 was mainly associated with the 50S subunit of the ribosome. Absence of Lmo1722 decreased the fraction of 50S ribosomal subunits and mature 70S ribosomes and affected the processing of the 23S precursor rRNA. The ribosomal profile could be restored to wild-type levels in a Δlmo1722 strain expressing Lmo1722. Interestingly, the C-terminal part of Lmo1722 was redundant for low-temperature growth, motility, 23S rRNA processing, and appropriate ribosomal maturation. However, Lmo1722 lacking the C terminus showed a reduced affinity for the 50S and 70S fractions, suggesting that the C terminus is important for proper guidance of Lmo1722 to the 50S subunit. Taken together, our results show that the Listeria RNA helicase Lmo1722 is essential for growth at low temperatures, motility, and rRNA processing and is important for ribosomal maturation, being associated mainly with the 50S subunit of the ribosome.

  16. Studies of the effects of ultraviolet radiation on the structural integrities of ribosomal RNA components of the Escherichia coli 50S ribosomal subunit

    International Nuclear Information System (INIS)

    Gorelic, L.; Parker, D.

    1978-01-01

    The effects of 254-nm radiation on the structural integrities of free and 50S ribosome-bound 5S and 23S ribosomal ribonucleic acids (rRNA) have been elucidated. Irradiation of aqueous solutions of Escherichia coli 50S ribosomes with 253.7-nm radiation results in the formation of single-strand breaks in double-stranded regions of the 23S rRNA component, but not in rRNA chain scission, and destabilization of the secondary structure of the 23S rRNA toward denaturation. The minimum doses of 253.7-nm radiation required for the first detection of the two effects are 7 x 10 19 quanta for the production of single-strand breaks in double-stranded regions of the 23S rRNA, and 19 quanta for destabilization of the 23S rRNA secondary structure. Free 23S rRNA is resistant toward photoinduced chain breakage at doses of 253.7-nm radiation up to at least 2.3 x 10 20 and is much less sensitive toward destabilization of secondary structure than ribosome-bound 23S rRNA. In contrast to the photosensitivity of 50S ribosome-bound 23S rRNA toward chain breakage, 50S ribosome-bound 5S rRNA is resistant toward chain breakage at doses of 253.7-nm radiation up to at least 2.3 x 10 20 quanta. Ribosome-bound 5S and 23S rRNA are also not photosensitive toward intermolecular 5S/23S rRNA cross-linkage

  17. cDNA, genomic sequence cloning and analysis of the ribosomal ...

    African Journals Online (AJOL)

    Ribosomal protein L37A (RPL37A) is a component of 60S large ribosomal subunit encoded by the RPL37A gene, which belongs to the family of ribosomal L37AE proteins, located in the cytoplasm. The complementary deoxyribonucleic acid (cDNA) and the genomic sequence of RPL37A were cloned successfully from giant ...

  18. Tibial and Femoral Tunnel Changes After ACL Reconstruction: A Prospective 2-Year Longitudinal MRI Study.

    Science.gov (United States)

    Weber, Alexander E; Delos, Demetris; Oltean, Hanna N; Vadasdi, Katherine; Cavanaugh, John; Potter, Hollis G; Rodeo, Scott A

    2015-05-01

    Tunnel widening after anterior cruciate ligament reconstruction (ACL-R) is a well-accepted and frequent phenomenon, yet little is known regarding its origin or natural history. To prospectively evaluate the cross-sectional area (CSA) changes in tibial and femoral bone tunnels after ACL-R with serial MRI. Case series; Level of evidence, 4. Patients underwent arthroscopic ACL-R with the same surgeon, surgical technique, and rehabilitation protocol. Each patient underwent preoperative dual-energy x-ray absorptiometry and clinical evaluation, as well as postoperative time zero MRI followed by subsequent MRI and clinical examination, including functional and subjective outcome tests, at 6, 12, 24, 52, and 104 weeks. Tibial and femoral tunnel CSA was measured on each MRI at tunnel aperture (ttA and ftA), midsection (ttM and ftM), and exit (ttE and ftE). Logistic regression modeling was used to examine the predictive value of demographic data and preoperative bone quality (as measured by dual-energy x-ray absorptiometry) on functional outcome scores, manual and instrumented laxity measurements, and changes in tunnel area over time. Eighteen patients (including 12 men), mean age 35.5±8.7 years, underwent ACL-R. There was significant tunnel expansion at ttA and ftA sites 6 weeks postoperatively (P=.024 and .0045, respectively). Expansion continued for 24 weeks, with progressive tunnel narrowing thereafter. Average ttA CSA was significantly larger than ftA CSA at all times. The ttM significantly expanded after 6 weeks (P=.06); continued expansion to week 12 was followed by 21 months of reduction in tunnel diameter. The ftM and both ttE and ftE sites decreased in CSA over the 2 years. Median Lysholm and International Knee Documentation Committee scores significantly improved at final follow-up (P=.0083 and 1 year from time of injury) predicted increased tunnel widening and accelerated expansion in CSA (Pclinical outcome. Younger age, male sex, and delay from injury to ACL

  19. Control of ribosome traffic by position-dependent choice of synonymous codons

    DEFF Research Database (Denmark)

    Mitarai, Namiko; Pedersen, Steen

    2013-01-01

    Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino...... acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby...... ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated...

  20. Charge Segregation and Low Hydrophobicity Are Key Features of Ribosomal Proteins from Different Organisms*

    Science.gov (United States)

    Fedyukina, Daria V.; Jennaro, Theodore S.; Cavagnero, Silvia

    2014-01-01

    Ribosomes are large and highly charged macromolecular complexes consisting of RNA and proteins. Here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. We examined 50 S ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. We found that ∼67% ribosomal proteins from halophiles are negatively charged, whereas only up to ∼15% of ribosomal proteins from non-halophiles share this property. Conversely, hydrophobicity tends to be lower for ribosomal proteins from halophiles than for the corresponding proteins from non-halophiles. Importantly, the surface electrostatic potential of ribosomal proteins from all organisms, especially halophiles, has distinct positive and negative regions across all the examined species. Positively and negatively charged residues of ribosomal proteins tend to be clustered in buried and solvent-exposed regions, respectively. Hence, the majority of ribosomal proteins is characterized by a significant degree of intramolecular charge segregation, regardless of the organism of origin. This key property enables the ribosome to accommodate proteins within its complex scaffold regardless of their overall net charge. PMID:24398678

  1. Exit channels of autoionization resonances in atoms

    International Nuclear Information System (INIS)

    Krause, M.O.

    1985-01-01

    In many-electron atoms with open shells strong autoionization resonances occur when an electron from an inner, weakly bound subshell is excited. Usually, the resonance state lies above several ionization thresholds and, hence, will decay into more than one exit or continuum channel. Several cases are discussed in which the resonance state is induced by synchrotron radiation, and the exit channels are differentiated and characterized by the analysis of the ejected electrons

  2. GTPases and the origin of the ribosome

    Directory of Open Access Journals (Sweden)

    Smith Temple F

    2010-05-01

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

  3. A CFD-based aerodynamic design procedure for hypersonic wind-tunnel nozzles

    Science.gov (United States)

    Korte, John J.

    1993-01-01

    A new procedure which unifies the best of current classical design practices, computational fluid dynamics (CFD), and optimization procedures is demonstrated for designing the aerodynamic lines of hypersonic wind-tunnel nozzles. The new procedure can be used to design hypersonic wind tunnel nozzles with thick boundary layers where the classical design procedure has been shown to break down. An efficient CFD code, which solves the parabolized Navier-Stokes (PNS) equations using an explicit upwind algorithm, is coupled to a least-squares (LS) optimization procedure. A LS problem is formulated to minimize the difference between the computed flow field and the objective function, consisting of the centerline Mach number distribution and the exit Mach number and flow angle profiles. The aerodynamic lines of the nozzle are defined using a cubic spline, the slopes of which are optimized with the design procedure. The advantages of the new procedure are that it allows full use of powerful CFD codes in the design process, solves an optimization problem to determine the new contour, can be used to design new nozzles or improve sections of existing nozzles, and automatically compensates the nozzle contour for viscous effects as part of the unified design procedure. The new procedure is demonstrated by designing two Mach 15, a Mach 12, and a Mach 18 helium nozzles. The flexibility of the procedure is demonstrated by designing the two Mach 15 nozzles using different constraints, the first nozzle for a fixed length and exit diameter and the second nozzle for a fixed length and throat diameter. The computed flow field for the Mach 15 least squares parabolized Navier-Stokes (LS/PNS) designed nozzle is compared with the classically designed nozzle and demonstrates a significant improvement in the flow expansion process and uniform core region.

  4. Control of the mitotic exit network during meiosis

    Science.gov (United States)

    Attner, Michelle A.; Amon, Angelika

    2012-01-01

    The mitotic exit network (MEN) is an essential GTPase signaling pathway that triggers exit from mitosis in budding yeast. We show here that during meiosis, the MEN is dispensable for exit from meiosis I but contributes to the timely exit from meiosis II. Consistent with a role for the MEN during meiosis II, we find that the signaling pathway is active only during meiosis II. Our analysis further shows that MEN signaling is modulated during meiosis in several key ways. Whereas binding of MEN components to spindle pole bodies (SPBs) is necessary for MEN signaling during mitosis, during meiosis MEN signaling occurs off SPBs and does not require the SPB recruitment factor Nud1. Furthermore, unlike during mitosis, MEN signaling is controlled through the regulated interaction between the MEN kinase Dbf20 and its activating subunit Mob1. Our data lead to the conclusion that a pathway essential for vegetative growth is largely dispensable for the specialized meiotic divisions and provide insights into how cell cycle regulatory pathways are modulated to accommodate different modes of cell division. PMID:22718910

  5. Turbine-missile casing exit tests

    International Nuclear Information System (INIS)

    Yoshimura, H.R.; Sliter, G.E.

    1978-01-01

    Nuclear power plant designers are required to provide safety-related components with adequate protection against hypothetical turbine-missile impacts. In plants with a ''peninsula'' arrangement, protection is provided by installing the turbine axis radially from the reactor building, so that potential missile trajectories are not in line with the plant. In plants with a ''non-peninsula'' arrangement (turbine axis perpendicular to a radius), designers rely on the low probability of a missile strike and on the protection provided by reinforced concrete walls in order to demonstrate an adequate level of protection USNRC Regulatory Guide 1.115). One of the critical first steps in demonstrating adequacy is the determination of the energy and spin of the turbine segments as they exit the turbine casing. The spin increases the probability that a subsequent impact with a protective barrier will be off-normal and therefore less severe than the normal impact assumed in plant designs. Two full-scale turbine-missile casing exit tests which were conducted by Sandia Laboratories at their rocket-sled facility in Albuquerque, New Mexico, are described. Because of wide variations in turbine design details, postulated failure conditions, and missile exit scenarios, the conditions for the two tests were carefully selected to be as prototypical as possible, while still maintaining the well-controlled and well-characterized test conditions needed for generating benchmark data

  6. Entry and Exit.

    Science.gov (United States)

    1987-03-01

    1. Introduction R Analyses of industrial competition have attained a new vigor with the application of game -theoretic methods. The process of... competition is represented in models that reflect genuine struggles for entry, market power, and continuing survival. Dynamics and informational effects are...presents a few of the models developed recently to study competitive processes that affect a firm’s entry into a market , and the decision to exit. The

  7. Exiting and Returning to the Parental Home for Boomerang Kids.

    Science.gov (United States)

    Sandberg-Thoma, Sara E; Snyder, Anastasia R; Jang, Bohyun Joy

    2015-06-01

    Young adults commonly exit from and return to the parental home, yet few studies have examined the motivation behind these exits and returns using a life course framework. Using data from the National Longitudinal Survey of Youth 1997, the authors examined associations between mental health problems and economic characteristics and exits from (n = 8,162), and returns to (n = 6,530), the parental home during the transition to adulthood. The average age of the respondents was 24 years. The authors found evidence that mental health and economic characteristics were related to home leaving and returning. Emotional distress was associated with earlier exits from, and returns to, the parental home; alcohol problems were associated with earlier returns to the parental home. The findings regarding economic resources were unexpectedly mixed. Greater economic resources were linked to delayed exits from, and earlier returns to, the parental home. The implications of these findings for young adults are discussed.

  8. Ribosomal trafficking is reduced in Schwann cells following induction of myelination

    Directory of Open Access Journals (Sweden)

    James M. Love

    2015-08-01

    Full Text Available Local synthesis of proteins within the Schwann cell periphery is extremely important for efficient process extension and myelination, when cells undergo dramatic changes in polarity and geometry. Still, it is unclear how ribosomal distributions are developed and maintained within Schwann cell projections to sustain local translation. In this multi-disciplinary study, we expressed a plasmid encoding a fluorescently labeled ribosomal subunit (L4-GFP in cultured primary rat Schwann cells. This enabled the generation of high-resolution, quantitative data on ribosomal distributions and trafficking dynamics within Schwann cells during early stages of myelination, induced by ascorbic acid treatment. Ribosomes were distributed throughout Schwann cell projections, with ~2-3 bright clusters along each projection. Clusters emerged within 1 day of culture and were maintained throughout early stages of myelination. Three days after induction of myelination, net ribosomal movement remained anterograde (directed away from the Schwann cell body, but ribosomal velocity decreased to about half the levels of the untreated group. Statistical and modeling analysis provided additional insight into key factors underlying ribosomal trafficking. Multiple regression analysis indicated that net transport at early time points was dependent on anterograde velocity, but shifted to dependence on anterograde duration at later time points. A simple, data-driven rate kinetics model suggested that the observed decrease in net ribosomal movement was primarily dictated by an increased conversion of anterograde particles to stationary particles, rather than changes in other directional parameters. These results reveal the strength of a combined experimental and theoretical approach in examining protein localization and transport, and provide evidence of an early establishment of ribosomal populations within Schwann cell projections with a reduction in trafficking following

  9. Expanding the ribosomal universe.

    Science.gov (United States)

    Dinman, Jonathan D; Kinzy, Terri Goss

    2009-12-09

    In this issue of Structure, Taylor et al. (2009) present the most complete model of an eukaryotic ribosome to date. This achievement represents a critical milestone along the path to structurally defining the unique aspects of the eukaryotic protein synthetic machinery.

  10. Shored gunshot wound of exit. A phenomenon with identity crisis.

    Science.gov (United States)

    Aguilar, J C

    1983-09-01

    Shored gunshot wound of exit is produced when the outstretched skin is impaled, sandwiched, and crushed between the outgoing bullet and the unyielding object over the exit site, thus leaving an abrasion collar on the wound margin. Proper coaptation of the wound margin is impossible because of the loss of skin just like those observed in entrance wounds. In contrast to the entrance wound, the supported exit wound shows a scalloped or punched-out abrasion collar and sharply contoured skin in between the radiating skin lacerations marginating the abrasion (Fig. 1). Should gunpowder be observed around the exit site, it is often unevenly distributed, and is not associated with searing, gunpowder stippled abrasion, tatooing, and deposition of soot.

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

    Directory of Open Access Journals (Sweden)

    Jendrik Hentschel

    2017-07-01

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

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

    Science.gov (United States)

    Hentschel, Jendrik; Burnside, Chloe; Mignot, Ingrid; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad

    2017-07-05

    The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Control of ribosome traffic by position-dependent choice of synonymous codons

    International Nuclear Information System (INIS)

    Mitarai, Namiko; Pedersen, Steen

    2013-01-01

    Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of ‘traffic jams’ where multiple ribosomes collide and form queues. To test this ‘context effect’ further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species. (paper)

  14. Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data.

    Science.gov (United States)

    Wang, Hao; Kingsford, Carl; McManus, C Joel

    2018-03-15

    Ribosome profiling has emerged as a powerful technique to study mRNA translation. Ribosome profiling has the potential to determine the relative quantities and locations of ribosomes on mRNA genome wide. Taking full advantage of this approach requires accurate measurement of ribosome locations. However, experimental inconsistencies often obscure the positional information encoded in ribosome profiling data. Here, we describe the Ribodeblur pipeline, a computational analysis tool that uses a maximum likelihood framework to infer ribosome positions from heterogeneous datasets. Ribodeblur is simple to install, and can be run on an average modern Mac or Linux-based laptop. We detail the process of applying the pipeline to high-coverage ribosome profiling data in yeast, and discuss important considerations for potential extension to other organisms. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Expression of ribosomal genes in pea cotyledons at the initial stages of germination

    International Nuclear Information System (INIS)

    Gumilevskaya, N.A.; Chumikhina, L.V.; Akhmatova, A.T.; Kretovich, V.L.

    1986-01-01

    The time of appearance of newly synthesized rRNAs and ribosomal proteins (r-proteins) in the ribosomes of pea cotyledons (Pisum sativum L.) during germination was investigated. The ribosomal fraction was isolated and analyzed according to the method of germination of the embryo in the presence of labeled precursors or after pulse labeling of the embryos at different stages of germination. For the identification of newly synthesized rRNAs in the ribosomes we estimated the relative stability of labeled RNAs to the action of RNase, the sedimentation rate, the ability to be methylated in vivo in the presence of [ 14 C]CH 3 -methionine, and the localization in the subunits of dissociated ribosomes. The presence of newly synthesized r-proteins in the ribosomes was judged on the basis of the electrophoretic similarity in SDS-disc electrophoresis of labeled polypeptides of purified ribosome preparations and of genuine r-proteins, as well as according to the localization of labeled proteins in the subunits of the dissociated ribosomes. It was shown that the expression of the ribosomal genes in highly specialized cells of pea cotyledons that have completed their growth occurs at very early stages of germination

  16. Exit and Voice: Organizational Loyalty and Dispute Resolution Strategies

    Science.gov (United States)

    Hoffmann, Elizabeth A.

    2006-01-01

    This study compares workplace dispute resolution strategies (exit, voice and toleration) in matched pairs of conventional and worker-owned cooperative organizations operating in three industries--coal mining, taxicab driving and organic food distribution. Building on Hirschman's classic exit, voice and loyalty thesis, this research demonstrates…

  17. Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World?

    Directory of Open Access Journals (Sweden)

    Ilana C. Agmon

    2016-12-01

    Full Text Available An indispensable prerequisite for establishing a scenario of life emerging by natural processes is the requirement that the first simple proto-molecules could have had a realistic probability of self-assembly from random molecular polymers in the prebiotic world. The vestige of the proto-ribosome, which is believed to be still embedded in the contemporary ribosome, is used to assess the feasibility of such spontaneous emergence. Three concentric structural elements of different magnitudes, having a dimeric nature derived from the symmetrical region of the ribosomal large subunit, were suggested to constitute the vestige of the proto-ribosome. It is assumed to have materialized spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and simple elongation. Probabilistic and energetic considerations are applied in order to evaluate the suitability of the three contenders for being the initial proto-ribosome. The analysis points to the simplest proto-ribosome, comprised of a dimer of tRNA-like molecules presently embedded in the core of the symmetrical region, as the only one having a realistic statistical likelihood of spontaneous emergence from random RNA chains. Hence it offers a feasible starting point for a continuous evolutionary path from the prebiotic matter, through natural processes, into the intricate modern translation system.

  18. Lingering illness or sudden death? Pre-exit employment developments in German establishments

    OpenAIRE

    Fackler, Daniel; Schnabel, Claus; Wagner, Joachim

    2012-01-01

    Using a large administrative dataset for Germany, this paper compares employment developments in exiting and surviving establishments. For both West and East Germany we find a clear 'shadow of death' effect reflecting lingering illness: establishments shrink dramatically already several years before closure, employment growth rates differ strongly between exiting and surviving establishments, and this difference becomes stronger as exit approaches. We further show that prior to exit the workf...

  19. Phosphorylation of ribosomal proteins induced by auxins in maize embryonic tissues

    International Nuclear Information System (INIS)

    Perez, L.; Aguilar, R.; Mendez, A.P.; de Jimenez, E.S.

    1990-01-01

    The effect of auxin on ribosomal protein phosphorylation of germinating maize (Zea mays) tissues was investigated. Two-dimensional gel electrophoresis and autoradiography of [ 32 P] ribosomal protein patterns for natural and synthetic auxin-treated tissues were performed. Both the rate of 32 P incorporation and the electrophoretic patterns were dependent on 32 P pulse length, suggesting that active protein phosphorylation-dephosphorylation occurred in small and large subunit proteins, in control as well as in auxin-treated tissues. The effect of ribosomal protein phosphorylation on in vitro translation was tested. Measurements of poly(U) translation rates as a function of ribosome concentration provided apparent K m values significantly different for auxin-treated and nontreated tissues. These findings suggest that auxin might exert some kind of translational control by regulating the phosphorylated status of ribosomal proteins

  20. Analysis of unexpected exits using the Fokker - Planck equation

    NARCIS (Netherlands)

    Herwaarden, van O.A.

    1996-01-01


    In this thesis exit problems are considered for stochastic dynamical systems with small random fluctuations. We study exit from a domain in the state space through a boundary, or a specified part of the boundary, that is unattainable in the underlying deterministic system. We analyze

  1. Static thrust-vectoring performance of nonaxisymmetric convergent-divergent nozzles with post-exit yaw vanes. M.S. Thesis - George Washington Univ., Aug. 1988

    Science.gov (United States)

    Foley, Robert J.; Pendergraft, Odis C., Jr.

    1991-01-01

    A static (wind-off) test was conducted in the Static Test Facility of the 16-ft transonic tunnel to determine the performance and turning effectiveness of post-exit yaw vanes installed on two-dimensional convergent-divergent nozzles. One nozzle design that was previously tested was used as a baseline, simulating dry power and afterburning power nozzles at both 0 and 20 degree pitch vectoring conditions. Vanes were installed on these four nozzle configurations to study the effects of vane deflection angle, longitudinal and lateral location, size, and camber. All vanes were hinged at the nozzle sidewall exit, and in addition, some were also hinged at the vane quarter chord (double-hinged). The vane concepts tested generally produced yaw thrust vectoring angles much less than the geometric vane angles, for (up to 8 percent) resultant thrust losses. When the nozzles were pitch vectored, yawing effectiveness decreased as the vanes were moved downstream. Thrust penalties and yawing effectiveness both decreased rapidly as the vanes were moved outboard (laterally). Vane length and height changes increased yawing effectiveness and thrust ratio losses, while using vane camber, and double-hinged vanes increased resultant yaw angles by 50 to 100 percent.

  2. Going, Going, Gone. Innovation and Exit in Manufacturing Firms

    NARCIS (Netherlands)

    E. Cefis (Elena); O. Marsili (Orietta)

    2007-01-01

    textabstractThis paper examines the effect of innovation on the risk of exit of a firm, distinguishing between different modes of exits. Innovation represents a resource and a capability that helps a firm to build competitive advantage and remain in the market. At the same time, the resources and

  3. Comparison of sources of exit fluence variation for IMRT

    International Nuclear Information System (INIS)

    Gardner, Joseph K; Gordon, J James; Wang Song; Siebers, Jeffrey V; Clews, Luke; Greer, Peter B

    2009-01-01

    The fluence exiting a patient during beam delivery can be used as treatment delivery quality assurance, either by direct comparison with expected exit fluences or by backprojection to reconstruct the patient dose. Multiple possible sources of measured exit fluence deviations exist, including changes in the beam delivery and changes in the patient anatomy. The purpose of this work is to compare the deviations caused by these sources. Machine delivery-related variability is measured by acquiring multiple dosimetric portal images (DPIs) of several test fields without a patient/phantom in the field over a time period of 2 months. Patient anatomy-related sources of fluence variability are simulated by computing transmission DPIs for a prostate patient using the same incident fluence for 11 different computed tomography (CT) images of the patient anatomy. The standard deviation (SD) and maximum deviation of the exit fluence, averaged over 5 mm x 5 mm square areas, is calculated for each test set. Machine delivery fluence SDs as large as 1% are observed for a sample patient field and as large as 2.5% for a picket-fence dMLC test field. Simulations indicate that day-to-day patient anatomy variations induce exit fluence SDs as large as 3.5%. The largest observed machine delivery deviations are 4% for the sample patient field and 7% for the picket-fence field, while the largest difference for the patient anatomy-related source is 8.5%. Since daily changes in patient anatomy can result in substantial exit fluence deviations, care should be taken when applying fluence back-projection to ensure that such deviations are properly attributed to their source. (note)

  4. Using an electronic portal imaging device for exit dose measurements in radiotherapy

    International Nuclear Information System (INIS)

    Ganowicz, M.; Wozniak, B.; Bekman, A.; Maniakowski, Z.

    2003-01-01

    To present a method of determining the exit dose with the use of an electronic portal imaging device (EPID). The device used was the Portal Vision LC250 (Varian). The EPID signals on the central beam axis have been related to the exit dose. The exit dose measurements were performed with the ionisation chamber in the slab phantom at the distance of dose maximum from the exit surface of the phantom. EPID reading was investigated as a function of field size, phantom thickness and source-detector distance. The relation between dose rate and the EPID reading is described with empirical functions applicable to the obtained data. The exit dose is calculated from the EPID reading as a product of the calibration factor and appropriate correction factors. The determination of the exit dose rate from the EPID signal requires the knowledge of many parameters and earlier determination of essential characteristics. (author)

  5. Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase.

    Science.gov (United States)

    Jha, Sujata; Rollins, Madeline G; Fuchs, Gabriele; Procter, Dean J; Hall, Elizabeth A; Cozzolino, Kira; Sarnow, Peter; Savas, Jeffrey N; Walsh, Derek

    2017-06-29

    Ribosomes have the capacity to selectively control translation through changes in their composition that enable recognition of specific RNA elements. However, beyond differential subunit expression during development, evidence for regulated ribosome specification within individual cells has remained elusive. Here we report that a poxvirus kinase phosphorylates serine/threonine residues in the human small ribosomal subunit protein, receptor for activated C kinase (RACK1), that are not phosphorylated in uninfected cells or cells infected by other viruses. These modified residues cluster in an extended loop in RACK1, phosphorylation of which selects for translation of viral or reporter mRNAs with 5' untranslated regions that contain adenosine repeats, so-called polyA-leaders. Structural and phylogenetic analyses revealed that although RACK1 is highly conserved, this loop is variable and contains negatively charged amino acids in plants, in which these leaders act as translational enhancers. Phosphomimetics and inter-species chimaeras have shown that negative charge in the RACK1 loop dictates ribosome selectivity towards viral RNAs. By converting human RACK1 to a charged, plant-like state, poxviruses remodel host ribosomes so that adenosine repeats erroneously generated by slippage of the viral RNA polymerase confer a translational advantage. Our findings provide insight into ribosome customization through trans-kingdom mimicry and the mechanics of species-specific leader activity that underlie poxvirus polyA-leaders.

  6. Miscoding-induced stalling of substrate translocation on the bacterial ribosome.

    Science.gov (United States)

    Alejo, Jose L; Blanchard, Scott C

    2017-10-10

    Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.

  7. Tunnel - history of

    International Nuclear Information System (INIS)

    1998-11-01

    This book introduces history of tunnel in ancient times, the middle ages and modern times, survey of tunnel and classification of bedrock like environment survey of position, survey of the ground, design of tunnel on basic thing of the design, and design of tunnel of bedrock, analysis of stability of tunnel and application of the data, construction of tunnel like lattice girder and steel fiber reinforced shot crete, and maintenance control and repair of tunnel.

  8. Structure based hypothesis of a mitochondrial ribosome rescue mechanism

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2012-05-01

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

  9. The determinants of firm exit in the French food industries

    OpenAIRE

    Blanchard, Pierre; Mathieu, Claude

    2012-01-01

    A semi-parametric approach is used to estimate firm propensity to exit. The unobserved individual productivity of a firm is first estimated using the Ackerberg et al. (2006) approach and then introduced as a determinant of firm exit in conjunction with other variables that may serve as barriers to exit, including the firm’s level of sunk costs and the industry concentration. Using an unbalanced panel of data for 5,849 firms in French food industries from 1996 to 2002, we find a signifi...

  10. Typical Underwater Tunnels in the Mainland of China and Related Tunneling Technologies

    Directory of Open Access Journals (Sweden)

    Kairong Hong

    2017-12-01

    Full Text Available In the past decades, many underwater tunnels have been constructed in the mainland of China, and great progress has been made in related tunneling technologies. This paper presents the history and state of the art of underwater tunnels in the mainland of China in terms of shield-bored tunnels, drill-and-blast tunnels, and immersed tunnels. Typical underwater tunnels of these types in the mainland of China are described, along with innovative technologies regarding comprehensive geological prediction, grouting-based consolidation, the design and construction of large cross-sectional tunnels with shallow cover in weak strata, cutting tool replacement under limited drainage and reduced pressure conditions, the detection and treatment of boulders, the construction of underwater tunnels in areas with high seismic intensity, and the treatment of serious sedimentation in a foundation channel of immersed tunnels. Some suggestions are made regarding the three potential great strait-crossing tunnels—the Qiongzhou Strait-Crossing Tunnel, Bohai Strait-Crossing Tunnel, and Taiwan Strait-Crossing Tunnel—and issues related to these great strait-crossing tunnels that need further study are proposed. Keywords: Underwater tunnel, Strait-crossing tunnel, Shield-bored tunnel, Immersed tunnel, Drill and blast

  11. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile.

    Directory of Open Access Journals (Sweden)

    Pierre Bonnin

    2017-05-01

    Full Text Available The well established phenomenon of ribosome drop-off plays crucial roles in translational accuracy and nutrient starvation responses during protein translation. When cells are under stress conditions, such as amino acid starvation or aminoacyl-tRNA depletion due to a high level of recombinant protein expression, ribosome drop-off can substantially affect the efficiency of protein expression. Here we introduce a mathematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant protein synthesis rate. Our results show that ribosome premature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' end. Importantly, the model predicts that the effects of ribosome drop-off on the translation rate are mRNA-specific, and we quantify their resilience to drop-off, showing that the mRNAs which present ribosome queues are much less affected by ribosome drop-off than those which do not. Moreover, among those mRNAs that do not present ribosome queues, resilience to drop-off correlates positively with the elongation rate, so that sequences using fast codons are expected to be less affected by ribosome drop-off. This result is consistent with a genome-wide analysis of S. cerevisiae, which reveals that under favourable growth conditions mRNAs coding for proteins involved in the translation machinery, known to be highly codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off. Moreover, in physiological conditions, the translation rate of mRNAs coding for regulatory, stress-related proteins, is less resilient to ribosome drop-off. This model therefore allows analysis of variations in the translational efficiency of individual mRNAs by accounting for the full range of known ribosome behaviours, as well as explaining mRNA-specific variations in ribosome density emerging from ribosome profiling

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

    Indian Academy of Sciences (India)

    Madhu

    all pathway of ribosome recycling in eubacteria with especial reference to the important role of the initiation factor ... [Seshadri A and Varshney U 2006 Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3 .... RRF binding results in a remarkable conformational change.

  13. Expression of protein-coding genes embedded in ribosomal DNA

    DEFF Research Database (Denmark)

    Johansen, Steinar D; Haugen, Peik; Nielsen, Henrik

    2007-01-01

    Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that e...... in the nucleolus....

  14. Backfilling of deposition tunnels: Use of bentonite pellets

    International Nuclear Information System (INIS)

    Dixon, David; Sanden, Torbjoern; Jonsson, Esther; Hansen, Johanna

    2011-02-01

    The state of knowledge related to use of bentonite pellets as part of backfill or other gap filling components in repository applications is reviewed. How the pellets interact with adjacent sealing materials and the surrounding rock mass is a critical aspect in determining backfill behaviour. The key features and processes that determine how the pellet component of the KBS-3V deposition tunnel backfill will behave are discussed and recommendations related to what additional information needs to be developed are provided. Experiences related to pellet material composition, size, shape, placement options and more importantly, the density to which they can be placed all indicate that there are significant limitations to the achievable as-placed density of bentonite pellet fill. Low as-placed density of the pellet fill component of the backfill is potentially problematic as the outermost regions of tunnel backfill will be the first region of the backfill to be contacted by water entering the tunnels. It is also through this region that initial water movement along the length of the deposition tunnels will occur. This will greatly influence the operations in a tunnel, especially with respect to situations where water is exiting the downstream face of still open deposition tunnels. Pellet-filled regions are also sensitive to groundwater salinity, susceptible to development of piping features and subsequent mechanical erosion by through flowing water, particularly in the period preceding deposition tunnel closure. A review of the experiences of various organisations considering use of bentonite-pellet materials as part of buffer or backfill barriers is provided in this document. From this information, potential options and limitations to use of pellets or pellet-granule mixtures in backfill are identified. Of particular importance is identification of the apparent upper-limits of dry density to which such materials can to be placed in the field. These bounds will

  15. Backfilling of deposition tunnels: Use of bentonite pellets

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, David (Atomic Energy of Canada Limited (Canada)); Sanden, Torbjoern (Clay Technology AB (Sweden)); Jonsson, Esther (Swedish Nuclear Fuel and Waste Mangaement Co. (Sweden)); Hansen, Johanna (Posiva Oy (Finland))

    2011-02-15

    The state of knowledge related to use of bentonite pellets as part of backfill or other gap filling components in repository applications is reviewed. How the pellets interact with adjacent sealing materials and the surrounding rock mass is a critical aspect in determining backfill behaviour. The key features and processes that determine how the pellet component of the KBS-3V deposition tunnel backfill will behave are discussed and recommendations related to what additional information needs to be developed are provided. Experiences related to pellet material composition, size, shape, placement options and more importantly, the density to which they can be placed all indicate that there are significant limitations to the achievable as-placed density of bentonite pellet fill. Low as-placed density of the pellet fill component of the backfill is potentially problematic as the outermost regions of tunnel backfill will be the first region of the backfill to be contacted by water entering the tunnels. It is also through this region that initial water movement along the length of the deposition tunnels will occur. This will greatly influence the operations in a tunnel, especially with respect to situations where water is exiting the downstream face of still open deposition tunnels. Pellet-filled regions are also sensitive to groundwater salinity, susceptible to development of piping features and subsequent mechanical erosion by through flowing water, particularly in the period preceding deposition tunnel closure. A review of the experiences of various organisations considering use of bentonite-pellet materials as part of buffer or backfill barriers is provided in this document. From this information, potential options and limitations to use of pellets or pellet-granule mixtures in backfill are identified. Of particular importance is identification of the apparent upper-limits of dry density to which such materials can to be placed in the field. These bounds will

  16. Computational resources for ribosome profiling: from database to Web server and software.

    Science.gov (United States)

    Wang, Hongwei; Wang, Yan; Xie, Zhi

    2017-08-14

    Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation. This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. At present, however, a comprehensive review on these resources is still lacking. Here, we survey the recent computational advances guided by ribosome profiling, with a focus on databases, Web servers and software tools for storing, visualizing and analyzing ribosome profiling data. This review is intended to provide experimental and computational biologists with a reference to make appropriate choices among existing resources for the question at hand. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number

    Directory of Open Access Journals (Sweden)

    Katherine I. Farley-Barnes

    2018-02-01

    Full Text Available Ribosome biogenesis is a highly regulated, essential cellular process. Although studies in yeast have established some of the biological principles of ribosome biogenesis, many of the intricacies of its regulation in higher eukaryotes remain unknown. To understand how ribosome biogenesis is globally integrated in human cells, we conducted a genome-wide siRNA screen for regulators of nucleolar number. We found 139 proteins whose depletion changed the number of nucleoli per nucleus from 2–3 to only 1 in human MCF10A cells. Follow-up analyses on 20 hits found many (90% to be essential for the nucleolar functions of rDNA transcription (7, pre-ribosomal RNA (pre-rRNA processing (16, and/or global protein synthesis (14. This genome-wide analysis exploits the relationship between nucleolar number and function to discover diverse cellular pathways that regulate the making of ribosomes and paves the way for further exploration of the links between ribosome biogenesis and human disease.

  18. Congenital Cervical Teratoma: Anaesthetic Management (The EXIT Procedure

    Directory of Open Access Journals (Sweden)

    Ferruh Bilgin

    2009-01-01

    Full Text Available Ex utero intrapartum treatment (EXIT is a procedure performed during caesarean section with preservation of fetal-placental circulation, which allows the safe handling of fetal airways with risk of airways obstruction. This report aimed at describing a case of anaesthesia for EXIT in a fetus with cervical teratoma. A 30-year-old woman, 70 kg, 160 cm, gravida 2, para 1, was followed because of polyhydramniosis diagnosed at 24 weeks′ gestation. During a routine ultrasonographic examination at 35 weeks′ gestation, it was noticed that the fetus had a tumoral mass on the anterior neck, the mass had cystic and calcified components and with a size of was 10 x 6 x5 cm. The patient with physical status ASA I, was submitted to caesarean section under general anaesthesia with mechanically controlled ventilation for exutero intrapartum treatment (EXIT. Anaesthesia was induced in rapid sequence with fentanyl, propofol and rocuronium and was maintained with isoflurane in 2.5 at 3 % in O 2 and N 2 O (50%. After hysterotomy, fetus was partially released assuring uterus-placental circulation, followed by fetal laryngoscopy and tracheal intuba-tion. The infant was intubated with an uncuffed, size 2.5 endotracheal tube. Excision of the mass was performed under general anaesthesia. After surgical intervention, on the fourth postoperative day, the infant was extubated and the newborn was discharged to the pediatric neonatal unit and on the seventh day postoperatively to home without complications. Major recommendations for EXIT are maternal-fetal safety, uterine relaxation to maintain uterine volume and uterus-placental circulation, and fetal immobility to help airway handling. We report one case of cervical teratoma managed successfully with EXIT procedure.

  19. The Effect of Exit Strategy on Optimal Portfolio Selection with Birandom Returns

    Directory of Open Access Journals (Sweden)

    Guohua Cao

    2013-01-01

    Full Text Available The aims of this paper are to use a birandom variable to denote the stock return selected by some recurring technical patterns and to study the effect of exit strategy on optimal portfolio selection with birandom returns. Firstly, we propose a new method to estimate the stock return and use birandom distribution to denote the final stock return which can reflect the features of technical patterns and investors' heterogeneity simultaneously; secondly, we build a birandom safety-first model and design a hybrid intelligent algorithm to help investors make decisions; finally, we innovatively study the effect of exit strategy on the given birandom safety-first model. The results indicate that (1 the exit strategy affects the proportion of portfolio, (2 the performance of taking the exit strategy is better than when the exit strategy is not taken, if the stop-loss point and the stop-profit point are appropriately set, and (3 the investor using the exit strategy become conservative.

  20. 30 CFR 56.4530 - Exits.

    Science.gov (United States)

    2010-07-01

    ... Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-SURFACE METAL AND NONMETAL MINES Fire Prevention and Control... a sufficient number of exits to permit prompt escape in case of fire. ...

  1. Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase centre

    DEFF Research Database (Denmark)

    Rosendahl, G; Douthwaite, S

    1993-01-01

    RNA, and to investigate how this interaction is influenced by other ribosomal components. Complexes were characterized in both naked 23 S rRNA and ribosomes from an E. coli L11-minus strain, before and after reconstitution with L11. The protein protects 17 riboses between positions 1058 and 1085 in the naked 23 S r......The Escherichia coli ribosomal protein (r-protein) L11 and its binding site on 23 S ribosomal RNA (rRNA) are associated with ribosomal hydrolysis of guanosine 5'-triphosphate (GTP). We have used hydroxyl radical footprinting to map the contacts between L11 and the backbone riboses in 23 S r......)4 and other proteins within the ribosome. The antibiotics thiostrepton and micrococcin inhibit the catalytic functions of this region by slotting in between the accessible loops and interacting with nucleotides there....

  2. STIMULATION METHODS IMPROVEMENT OF EXIT ROUTE ON RAILWAY TRANSPORT

    Directory of Open Access Journals (Sweden)

    A. I. Verlan

    2014-01-01

    Full Text Available Purpose. The purpose of the article is to assess the costs, which are redistributed in the system «shipper−railroad−consignee» during routing of rail transportation and the development of tariff simulation methods of shippers to the exit routes formation. Methodology. Using economic and mathematical analysis the distribution of costs among the various participants of transportation process during the exit routes formation is investigated in the article. Findings. For implementation of the tariff simulation methods of exit routes and retention of the existing tariff structure it is proposed to provide in the «Tariff catalogue for freight transportation by railway transport of Ukraine» the discount, differentiated from haulage distance. A new method for determining the fees amount for cars supply and removal on approach tracks by train locomotives was also offered. Originality. As a result of the research a new method for determination of the exit rout efficiency that, unlike the existing one, takes into account the various interests of the individual participants in the transportation process was proposed. The dependence of the correction factors to the tariff for freight transportation in their own cars by direct exit routes from distance haulage was obtained. Implementation of these coefficients provides an approximation of railway tariffs to the traffic handling costs. A method for determination the rate of fees for cars supply and removal on approach tracks by train locomotives was offered. Practical value. InUkraine creation of the tariff discounts system for freight transportation by exit routes consistent with international practice and allows bringing the tariff to the real traffic handling cost. This change on the one hand will provide stimulation for private capital investments in infrastructure development and shunting means of approach tracks, on the other – it will fix the shippers to the railroads and stop their outflow

  3. Photoaffinity labeling of rat liver ribosomes by N-(2-Nitro-4-azidobenzoyl)puromycin

    International Nuclear Information System (INIS)

    Boehm, H.; Stahl, J.; Bielka, H.

    1979-01-01

    N-(2-nitro-4-azidobenzoyl)-[ 3 H]puromycin (NAB-puromycin) was synthesized as a photoreactive derivative of puromycin in order to detect ribosomal proteins located near the peptidyltransferase centre of rat liver ribosomes. Irradiation of ribosome-NAB-puromycin complexes leads to covalent attachment of the affinity label to proteins of the large ribosomal subunit, in particular to proteins L28/29, and, to a somewhat lower extent, to proteins L4, L6, L10 and L24. The results are discussed in the light of earlier studies performed with other affinity labels that attacked the peptidyltransferase region of rat liver ribosomes. (author)

  4. Direct, coherent and incoherent intermediate state tunneling and scanning tunnel microscopy (STM)

    International Nuclear Information System (INIS)

    Halbritter, J.

    1997-01-01

    Theory and experiment in tunneling are still qualitative in nature, which hold true also for the latest developments in direct-, resonant-, coherent- and incoherent-tunneling. Those tunnel processes have recently branched out of the field of ''solid state tunnel junctions'' into the fields of scanning tunnel microscopy (STM), single electron tunneling (SET) and semiconducting resonant tunnel structures (RTS). All these fields have promoted the understanding of tunneling in different ways reaching from the effect of coherence, of incoherence and of charging in tunneling, to spin flip or inelastic effects. STM allows not only the accurate measurements of the tunnel current and its voltage dependence but, more importantly, the easy quantification via the (quantum) tunnel channel conductance and the distance dependence. This new degree of freedom entering exponentially the tunnel current allows an unique identification of individual tunnel channels and their quantification. In STM measurements large tunnel currents are observed for large distances d > 1 nm explainable by intermediate state tunneling. Direct tunneling with its reduced tunnel time and reduced off-site Coulomb charging bridges distances below 1 nm, only. The effective charge transfer process with its larger off-site and on-site charging at intermediate states dominates tunnel transfer in STM, biology and chemistry over distances in the nm-range. Intermediates state tunneling becomes variable range hopping conduction for distances larger than d > 2 nm, for larger densities of intermediate states n 1 (ε) and for larger temperatures T or voltages U, still allowing high resolution imaging

  5. In vivo labelling of functional ribosomes reveals spatial regulation during starvation in Podospora anserina

    Directory of Open Access Journals (Sweden)

    Silar Philippe

    2000-11-01

    Full Text Available Abstract Background To date, in eukaryotes, ribosomal protein expression is known to be regulated at the transcriptional and/or translational levels. But other forms of regulation may be possible. Results Here, we report the successful tagging of functional ribosomal particles with a S7-GFP chimaeric protein, making it possible to observe in vivo ribosome dynamics in the filamentous fungus Podospora anserina. Microscopic observations revealed a novel kind of ribosomal protein regulation during the passage between cell growth and stationary phases, with a transient accumulation of ribosomal proteins and/or ribosome subunits in the nucleus, possibly the nucleolus, being observed at the beginning of stationary phase. Conclusion Nuclear sequestration can be another level of ribosomal protein regulation in eukaryotic cells.This may contribute to the regulation of cell growth and division.

  6. In vivo labelling of functional ribosomes reveals spatial regulation during starvation in Podospora anserina

    Science.gov (United States)

    Lalucque, Hervé; Silar, Philippe

    2000-01-01

    Background To date, in eukaryotes, ribosomal protein expression is known to be regulated at the transcriptional and/or translational levels. But other forms of regulation may be possible. Results Here, we report the successful tagging of functional ribosomal particles with a S7-GFP chimaeric protein, making it possible to observe in vivo ribosome dynamics in the filamentous fungus Podospora anserina. Microscopic observations revealed a novel kind of ribosomal protein regulation during the passage between cell growth and stationary phases, with a transient accumulation of ribosomal proteins and/or ribosome subunits in the nucleus, possibly the nucleolus, being observed at the beginning of stationary phase. Conclusion Nuclear sequestration can be another level of ribosomal protein regulation in eukaryotic cells.This may contribute to the regulation of cell growth and division. PMID:11112985

  7. Dietary ascorbic acid normalizes ribosomal efficiency for collagen production in skin of streptozotocin-induced diabetic rats

    International Nuclear Information System (INIS)

    Schneir, M.; Imberman, M.; Ramamurthy, N.; Golub, L.

    1987-01-01

    The objective of this study was to quantify the contribution of both ribosome amount and ribosomal efficiency to decreased collagen production in skin of diabetic rats and diabetic rats treated with dietary ascorbic acid. Male Sprague-Dawley rats were distributed equally into the following categories: non-diabetic controls; diabetics; ascorbic acid-treated diabetics. On day-20, all rats were injected with ( 3 H)proline and killed after 2 h. Absolute rate of collagen production, ribosome content, and ribosomal efficiency of collagen production were quantified. Also ribosomal efficiency was quantified for ribosomes in sucrose-gradient fractionated post-mitochondrial supernatants. The results indicate that decreased ribosomal efficiency was responsible for 70% of the decreased collagen production with 30% caused by decreased ribosome content, when measured for total skin or sucrose gradient-isolated ribosomes. At both levels of analysis, ascorbic acid treatment normalized ribosomal efficiency, indicating diabetes-mediated decreased ribosomal efficiency for collagen production is related to a co-translational event, such as procollagen underhydroxylation

  8. Nature of radioactive contamination of components of ecosystems of streamflows from tunnels of Degelen massif

    International Nuclear Information System (INIS)

    Panitskiy, A.V.; Lukashenko, S.N.

    2015-01-01

    The paper provides data on environmental contamination due to radionuclides' migration with water. As a result of investigations there was obtained data on character of contamination of soil cover, surface water and underflow from tunnels of Degelen massif. Character of radionuclides' spatial distribution in environment was also shown. Mobility ranges of radionuclides' vertical and horizontal movements have been established in soils both across and along the stream flow. There was also shown a possibility to forecast radionuclides' concentration in soil by specific activity of these radionuclides in water. Different concentrations of radionuclides in associated components of the ecosystem (surface waters – ground waters – soils) have shown disequilibrium of their condition in this system. Generalization of investigation results for tunnel water streams' with water inflows, chosen as investigation objects in this work, allows to forecast radionuclides' behavior in meadow soils and other ecosystems of water streams from tunnels of Degelen test site. Based on analysis of curves, describing radionuclides' behavior in horizontal direction, we can forecast, that at this stage 137 Cs and 239+240 Pu would not be distributed more than 1.5 km from the access to the daylight surface, 90 Sr – not more than 2 km. - Highlights: • Contamination of soil cover, surface water and groundwater from tunnels of Degelen nuclear test area. • Radionuclides in associated components of the ecosystem showed disequilibrium. • Forecast that 137 Cs and 239+240 Pu will not be distributed more than 1.5 km from tunnel exits. • Forecast that 90 Sr will not be distributed more than 2 km

  9. Accuracy synthesis of T-shaped exit fixed mechanism in a double-crystal monochromator

    International Nuclear Information System (INIS)

    Wang Fengqin; Cao Chongzhen; Wang Jidai; Li Yushan; Gao Xueguan

    2007-01-01

    It is a key performance requirement for a double-crystal monochromator that the exit is fixed, and in order to improve the height accuracy of the exit in T-shaped exit fixed mechanism, the expression between the height of the exit and various original errors was put forward using geometrical analysis method. According to the independent action principle of original errors, accuracy synthesis of T-shaped exit fixed mechanism was studied by using the equal accuracy method, and the tolerance ranges of original errors were obtained. How to calculate the tolerance ranges of original errors was explained by giving an example. (authors)

  10. Technological Progress, Exit and Trade

    DEFF Research Database (Denmark)

    Schröder, Philipp; Sørensen, Allan

    productivity exporters are more likely to continue to export, and market exit is typically preceded by periods of contracting market shares. We show that the simple inclusion of exogenous economy wide technological progress into the standard Melitz (2003) model generates a tractable dynamic framework...

  11. Do spouses coordinate their work exits? A combined survey and register analysis from Norway.

    Science.gov (United States)

    Syse, Astri; Solem, Per Erik; Ugreninov, Elisabeth; Mykletun, Reidar; Furunes, Trude

    2014-09-01

    Research on spouses' joint work exits is scarce, although household factors such as spouses' work status, marital quality, and caregiving burdens are likely to affect seniors' work engagement. We therefore examine whether the work exit probability of one spouse affects that of the other. Discrete-time hazard regression analyses of survey data linked to later registry information including all gainfully employed married respondents aged 50-74 with a working spouse (N = 1,764) were used to assess subsequent work exits. A spouse's work exit is a strong predictor of a respondent's work exit (hazard ratio 3.1, 95% confidence interval [2.5, 4.0]). Educational attainment, poor marital quality, and spouses' health and care needs do not predict work exits. Surprisingly, no gender differences are observed. Research on larger survey samples to distinguish different work exit routes and reasons for spouses' joint work exits appears warranted. To account for cultural and welfare state characteristics, cross-national studies ought to be undertaken. © The Author(s) 2013.

  12. Differential antibiotic sensitivity determined by the large ribosomal subunit in thermophilic archaea.

    OpenAIRE

    Ruggero, D; Londei, P

    1996-01-01

    Hybrid ribosomes obtained by mixing the ribosomal subunits of the extremely thermophilic archaea Sulfolobus solfataricus and Desulfurococcus mobilis were tested for their sensitivity to selected antibiotics. It is shown that structural differences in the large ribosomal subunits determine qualitatively and quantitatively the patterns of response to alpha-sarcin and paromomycin in these species.

  13. Experiment of cavitation erosion at the exit of a long orifice

    Energy Technology Data Exchange (ETDEWEB)

    Yagi, Yoshinori; Murase, Michio [Inst. of Nuclear Safety System Inc., Mihama, Fukui (Japan)

    2002-09-01

    We performed experiments to clarify mechanism of cavitation erosion and to predict cavitation erosion rate at the exit of a long orifice equipped at the chemical and volume control system in a pressurized water reactor (PWR). In order to find this mechanism, we used a high speed video camera. As the result, we observed bubble collapses near the exit of the orifice when flow condition was oscillating. So the bubble collapses due to the oscillation might cause the first stage erosion at the exit of the orifice. Using the orifice which had the cone-shaped exit, we observed that bubbles collapsed near the exit and then they collapsed at the upstream like a chain reaction. So this bubble collapse mechanism could be explained as follows: shock wave was generated by the bubble collapse near the exit, then it propagated upwards, consequently it caused the bubble collapse at the upstream. And we predicted erosion rate by evaluating the effect of the velocity and comparing the erosion resistance between the test speciment (aluminum) and the plant material (stainless steel) by means of vibratory tests. We compared the predicted erosion rate with that of the average value estimated from plant investigation, then we examined the applicability of these method to the plant evaluations. (author)

  14. “Understanding exit from the founder’s business in family firms”

    OpenAIRE

    C. Salvato; F. Chirico; P. Sharma

    2010-01-01

    In this chapter we investigate the role of family-specific factors in facilitating or constraining business exit in family firms. Family business literature seems to have an implicit bias towards continuity and persistence in the founder’s business. This is explained by heavy emotional involvement and development of path-dependent core competences over generations. However, several long-lived family firms were able to successfully exit the founder’s business. Exit allowed them to free signifi...

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

    Directory of Open Access Journals (Sweden)

    Melody G Campbell

    2011-01-01

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

  16. Water-Exit Process Modeling and Added-Mass Calculation of the Submarine-Launched Missile

    Directory of Open Access Journals (Sweden)

    Yang Jian

    2017-11-01

    Full Text Available In the process that the submarine-launched missile exits the water, there is the complex fluid solid coupling phenomenon. Therefore, it is difficult to establish the accurate water-exit dynamic model. In the paper, according to the characteristics of the water-exit motion, based on the traditional method of added mass, considering the added mass changing rate, the water-exit dynamic model is established. And with help of the CFX fluid simulation software, a new calculation method of the added mass that is suit for submarine-launched missile is proposed, which can effectively solve the problem of fluid solid coupling in modeling process. Then by the new calculation method, the change law of the added mass in water-exit process of the missile is obtained. In simulated analysis, for the water-exit process of the missile, by comparing the results of the numerical simulation and the calculation of theoretical model, the effectiveness of the new added mass calculation method and the accuracy of the water-exit dynamic model that considers the added mass changing rate are verified.

  17. Collective behavior of mice passing through an exit under panic

    Science.gov (United States)

    Zhang, Teng; Zhang, Xuelin; Huang, Shenshi; Li, Changhai; Lu, Shouxiang

    2018-04-01

    Collective movement of animal in emergency condition has attracted growing attentions among researchers. However, many rules still need to be confirmed with adequate explanation. Study of collective behavior of mice can improve our understanding about the dynamics of pedestrian movement. However, its rules still need to be confirmed with adequate explanation. In this paper, collective behavior of mice passing through an exit under panic was investigated. The results showed that the total evacuation time decreased with exit width increasing in a certain range. Based on the different tendency of the curve in temporal evolution, the process of mice flow was divided into three stages. The density of mice near the exit peaks at a certain horizontal offset and starts to decrease over time. With the increase of the exit width, the duration of the higher density state decreased. We found that the frequency of time intervals obeyed a lognormal distribution or an exponential decay for different exit widths. In addition, the relationship between the group size and the group flow rate in different scenarios was analyzed. The phenomena found in our experiments show the collective behavioral characteristic of mice under panic. Our analysis in this paper will deepen our understanding of crowd dynamics in emergency condition.

  18. Proto-ribosome: a theoretical approach based on RNA relics

    OpenAIRE

    Demongeot, Jacques

    2017-01-01

    We describe in this paper, based on already published articles, a contribution to the theory postulating the existence of a proto-ribosome, which could have appeared early at the origin of life and we discuss the interest of this notion in an evolutionary perspective, taking into account the existence of possible RNA relics of this proto-ribosome.

  19. 30 CFR 57.4530 - Exits for surface buildings and structures.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Exits for surface buildings and structures. 57... Fire Prevention and Control Installation/construction/maintenance § 57.4530 Exits for surface buildings and structures. Surface buildings or structures in which persons work shall have a sufficient number...

  20. Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease.

    Science.gov (United States)

    Farrugia, Mark A; Wang, Beibei; Feig, Michael; Hausinger, Robert P

    2015-10-20

    Nickel-containing urease from Klebsiella aerogenes requires four accessory proteins for proper active site metalation. The metallochaperone UreE delivers nickel to UreG, a GTPase that forms a UreD/UreF/UreG complex, which binds to urease apoprotein via UreD. Prior in silico analysis of the homologous, structurally characterized UreH/UreF/UreG complex from Helicobacter pylori identified a water tunnel originating at a likely nickel-binding motif in UreG, passing through UreF, and exiting UreH, suggestive of a role for the channel in providing the metal to urease apoprotein for its activation; however, no experimental support was reported for the significance of this tunnel. Here, specific variants were designed to disrupt a comparable 34.6 Å predicted internal tunnel, alternative channels, and surface sites for UreD. Cells producing a set of tunnel-disrupting variants of UreD exhibited greatly reduced urease specific activities, whereas other mutants had no appreciable effect on activity. Affinity pull-down studies of cell-free extracts from tunnel-disrupting mutant cultures showed no loss of UreD interactions with urease or UreF/UreG. The nickel contents of urease samples enriched from activity-deficient cultures were decreased, while zinc and iron incorporation increased. Molecular dynamics simulations revealed size restrictions in the internal channels of the UreD variants. These findings support the role of a molecular tunnel in UreD as a direct facilitator of nickel transfer into urease, illustrating a new paradigm in active site metallocenter assembly.

  1. Exit, punishment and rewards in commons dilemmas: an experimental study.

    Directory of Open Access Journals (Sweden)

    Giangiacomo Bravo

    Full Text Available Commons dilemmas are interaction situations where a common good is provided or exploited by a group of individuals so that optimal collective outcomes clash with private interests. Although in these situations, social norms and institutions exist that might help individuals to cooperate, little is known about the interaction effects between positive and negative incentives and exit options by individuals. We performed a modified public good game experiment to examine the effect of exit, rewards and punishment, as well as the interplay between exit and rewards and punishment. We found that punishment had a stronger effect than rewards on cooperation if considered by itself, whereas rewards had a stronger effect when combined with voluntary participation. This can be explained in terms of the 'framing effect', i.e., as the combination of exit and rewards might induce people to attach higher expected payoffs to cooperative strategies and expect better behaviour from others.

  2. The activity of the acidic phosphoproteins from the 80 S rat liver ribosome.

    Science.gov (United States)

    MacConnell, W P; Kaplan, N O

    1982-05-25

    The selective removal of acidic phosphoproteins from the 80 S rat liver ribosome was accomplished by successive alcohol extractions at low salt concentration. The resulting core ribosomes lost over 90% of their translation activity and were unable to support the elongation factor 2 GTPase reaction. Both activities were partially restored when the dialyzed extracts were added back to the core ribosome. The binding of labeled adenosine diphosphoribosyl-elongation factor 2 to ribosomes was also affected by extraction and could be reconstituted, although not to the same extent as the GTPase activity associated with elongation factor 2 in the presence of the ribosome. The alcohol extracts of the 80 S ribosome contained mostly phosphoproteins P1 and P2 which could be dephosphorylated and rephosphorylated in solution by alkaline phosphatase and protein kinase, respectively. Dephosphorylation of the P1/P2 mixture in the extracts caused a decrease in the ability of these proteins to reactivate the polyphenylalanine synthesis activity of the core ribosome. However, treatment of the dephosphorylated proteins with the catalytic subunit of 3':5'-cAMP-dependent protein kinase in the presence of ATP reactivated the proteins when compared to the activity of the native extracts. Rabbit antisera raised against the alcohol-extracted proteins were capable of impairing both the polyphenylalanine synthesis reaction and the elongation factor 2-dependent GTPase reaction in the intact ribosomes.

  3. Monitoring pilot projects on bored tunnelling : The Second Heinenoord Tunnel and the Botlek Rail Tunnel

    NARCIS (Netherlands)

    Bakker, K.J.; De Boer, F.; Admiraal, J.B.M.; Van Jaarsveld, E.P.

    1999-01-01

    Two pilot projects for bored tunnelling in soft soil have been undertaken in the Netherlands. The monitoring was commissioned under the authority of the Centre for Underground Construction (COB). A description of the research related to the Second Heinenoord Tunnel and the Botlek Rail Tunnel will be

  4. Critical heat flux and exit film flow rate in a flow boiling system

    International Nuclear Information System (INIS)

    Ueda, Tatsuhiro; Isayama, Yasushi

    1981-01-01

    The critical heat flux in a flowing boiling system is an important problem in the evaporating tubes with high thermal load such as nuclear reactors and boilers, and gives the practical design limit. When the heat flux in uniformly heated evaporating tubes is gradually raised, the tube exit quality increases, and soon, the critical heat flux condition arises, and the wall temperature near tube exit rises rapidly. In the region of low exit quality, the critical heat flux condition is caused by the transition from nucleating boiling, and in the region of high exit quality, it is caused by dry-out. But the demarcation of both regions is not clear. In this study, for the purpose of obtaining the knowledge concerning the critical heat flux condition in a flowing boiling system, the relation between the critical heat flux and exit liquid film flow rate was examined. For the experiment, a uniformly heated vertical tube supplying R 113 liquid was used, and the measurement in the range of higher heating flux and mass velocity than the experiment by Ueda and Kin was carried out. The experimental setup and experimental method, the critical heat flux and exit quality, the liquid film flow rate at heating zone exit, and the relation between the critical heat flux and the liquid film flow rate at exit are described. (Kako, I.)

  5. Involvement of ribosomal protein L6 in assembly of functional 50S ribosomal subunit in Escherichia coli cells

    International Nuclear Information System (INIS)

    Shigeno, Yuta; Uchiumi, Toshio; Nomura, Takaomi

    2016-01-01

    Ribosomal protein L6, an essential component of the large (50S) subunit, primarily binds to helix 97 of 23S rRNA and locates near the sarcin/ricin loop of helix 95 that directly interacts with GTPase translation factors. Although L6 is believed to play important roles in factor-dependent ribosomal function, crucial biochemical evidence for this hypothesis has not been obtained. We constructed and characterized an Escherichia coli mutant bearing a chromosomal L6 gene (rplF) disruption and carrying a plasmid with an arabinose-inducible L6 gene. Although this ΔL6 mutant grew more slowly than its wild-type parent, it proliferated in the presence of arabinose. Interestingly, cell growth in the absence of arabinose was biphasic. Early growth lasted only a few generations (LI-phase) and was followed by a suspension of growth for several hours (S-phase). This suspension was followed by a second growth phase (LII-phase). Cells harvested at both LI- and S-phases contained ribosomes with reduced factor-dependent GTPase activity and accumulated 50S subunit precursors (45S particles). The 45S particles completely lacked L6. Complete 50S subunits containing L6 were observed in all growth phases regardless of the L6-depleted condition, implying that the ΔL6 mutant escaped death because of a leaky expression of L6 from the complementing plasmid. We conclude that L6 is essential for the assembly of functional 50S subunits at the late stage. We thus established conditions for the isolation of L6-depleted 50S subunits, which are essential to study the role of L6 in translation. - Highlights: • We constructed an in vivo functional assay system for Escherichia coli ribosomal protein L6. • Growth of an E. coli ΔL6 mutant was biphasic when L6 levels were depleted. • The ΔL6 mutant accumulated 50S ribosomal subunit precursors that sedimented at 45S. • L6 is a key player in the late stage of E. coli 50S subunit assembly.

  6. Involvement of ribosomal protein L6 in assembly of functional 50S ribosomal subunit in Escherichia coli cells

    Energy Technology Data Exchange (ETDEWEB)

    Shigeno, Yuta [Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567 (Japan); Uchiumi, Toshio [Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181 (Japan); Nomura, Takaomi, E-mail: nomurat@shinshu-u.ac.jp [Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567 (Japan)

    2016-04-22

    Ribosomal protein L6, an essential component of the large (50S) subunit, primarily binds to helix 97 of 23S rRNA and locates near the sarcin/ricin loop of helix 95 that directly interacts with GTPase translation factors. Although L6 is believed to play important roles in factor-dependent ribosomal function, crucial biochemical evidence for this hypothesis has not been obtained. We constructed and characterized an Escherichia coli mutant bearing a chromosomal L6 gene (rplF) disruption and carrying a plasmid with an arabinose-inducible L6 gene. Although this ΔL6 mutant grew more slowly than its wild-type parent, it proliferated in the presence of arabinose. Interestingly, cell growth in the absence of arabinose was biphasic. Early growth lasted only a few generations (LI-phase) and was followed by a suspension of growth for several hours (S-phase). This suspension was followed by a second growth phase (LII-phase). Cells harvested at both LI- and S-phases contained ribosomes with reduced factor-dependent GTPase activity and accumulated 50S subunit precursors (45S particles). The 45S particles completely lacked L6. Complete 50S subunits containing L6 were observed in all growth phases regardless of the L6-depleted condition, implying that the ΔL6 mutant escaped death because of a leaky expression of L6 from the complementing plasmid. We conclude that L6 is essential for the assembly of functional 50S subunits at the late stage. We thus established conditions for the isolation of L6-depleted 50S subunits, which are essential to study the role of L6 in translation. - Highlights: • We constructed an in vivo functional assay system for Escherichia coli ribosomal protein L6. • Growth of an E. coli ΔL6 mutant was biphasic when L6 levels were depleted. • The ΔL6 mutant accumulated 50S ribosomal subunit precursors that sedimented at 45S. • L6 is a key player in the late stage of E. coli 50S subunit assembly.

  7. First Degree Pacemaker Exit Block

    Directory of Open Access Journals (Sweden)

    Johnson Francis

    2016-10-01

    Full Text Available Usually atrial and ventricular depolarizations follow soon after the pacemaker stimulus (spike on the ECG. But there can be an exit block due to fibrosis at the electrode - tissue interface at the lead tip. This can increase the delay between the spike and atrial or ventricular depolarization.

  8. Exit Planning At Joost El

    DEFF Research Database (Denmark)

    Nellemann, Camilla

    2017-01-01

    This is a Danish version. This case focuses on an owner-manager's considerations regarding his exit. Carsten Joost established Joost El in 2005. It currently employs 10 people. He has two sons but no intention to hand over the business to them. Rather, he hopes that his key employee eventually...

  9. Effects of injection nozzle exit width on rotating detonation engine

    Science.gov (United States)

    Sun, Jian; Zhou, Jin; Liu, Shijie; Lin, Zhiyong; Cai, Jianhua

    2017-11-01

    A series of numerical simulations of RDE modeling real injection nozzles with different exit widths are performed in this paper. The effects of nozzle exit width on chamber inlet state, plenum flowfield and detonation propagation are analyzed. The results are compared with that using an ideal injection model. Although the ideal injection model is a good approximation method to model RDE inlet, the two-dimensional effects of real nozzles are ignored in the ideal injection model so that some complicated phenomena such as the reflected waves caused by the nozzle walls and the reversed flow into the nozzles can not be modeled accurately. Additionally, the ideal injection model overpredicts the block ratio. In all the cases that stabilize at one-wave mode, the block ratio increases as the nozzle exit width gets smaller. The dual-wave mode case also has a relatively high block ratio. A pressure oscillation in the plenum with the same main frequency with the rotating detonation wave is observed. A parameter σ is applied to describe the non-uniformity in the plenum. σ increases as the nozzle exit width gets larger. Under some condition, the heat release on the interface of fresh premixed gas layer and detonation products can be strong enough to induce a new detonation wave. A spontaneous mode-transition process is observed for the smallest exit width case. Due to the detonation products existing in the premixed gas layer before the detonation wave, the detonation wave will propagate through reactants and products alternately, and therefore its strength will vary with time, especially near the chamber inlet. This tendency gets weaker as the injection nozzle exit width increases.

  10. Senescent changes in the ribosomes of animal cells in vivo and in vitro

    Science.gov (United States)

    Miquel, J.; Johnson, J. E., Jr.

    1979-01-01

    The paper examines RNA-ribosomal changes observed in protozoa and fixed postmitotic cells, as well as the characteristics of intermitotic cells. Attention is given to a discussion of the implications of the reported ribosomal changes as to the senescent deterioration of protein synthesis and physiological functions. A survey of the literature suggests that, while the data on ribosomal change in dividing cells both in vivo and in vitro are inconclusive, there is strong histological and biochemical evidence in favor of some degree of quantitative ribosomal loss in fixed postmitotic cells. Since these decreases in ribosomes are demonstrated in differential cells from nematodes, insects and mammals, they may represent a universal manifestation of cytoplasmic senescence in certain types of fixed postmitotic animal cells. The observed variability in ribosomal loss for cells belonging to the same type suggests that this involution phenomenon is rather related to the wear and tear suffered by a particular cell.

  11. DNA replication stress restricts ribosomal DNA copy number.

    Science.gov (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

    2017-09-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  12. DNA replication stress restricts ribosomal DNA copy number

    Science.gov (United States)

    Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

    2017-01-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

  13. DNA replication stress restricts ribosomal DNA copy number.

    Directory of Open Access Journals (Sweden)

    Devika Salim

    2017-09-01

    Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  14. Revisit the faster-is-slower effect for an exit at a corner

    Science.gov (United States)

    Chen, Jun Min; Lin, Peng; Wu, Fan Yu; Li Gao, Dong; Wang, Guo Yuan

    2018-02-01

    The faster-is-slower effect (FIS), which means that crowd at a high enough velocity could significantly increase the evacuation time to escape through an exit, is an interesting phenomenon in pedestrian dynamics. Such phenomenon had been studied widely and has been experimentally verified in different systems of discrete particles flowing through a centre exit. To experimentally validate this phenomenon by using people under high pressure is difficult due to ethical issues. A mouse, similar to a human, is a kind of self-driven and soft body creature with competitive behaviour under stressed conditions. Therefore, mice are used to escape through an exit at a corner. A number of repeated tests are conducted and the average escape time per mouse at different levels of stimulus are analysed. The escape times do not increase obviously with the level of stimulus for the corner exit, which is contrary to the experiment with the center exit. The experimental results show that the FIS effect is not necessary a universal law for any discrete system. The observation could help the design of buildings by relocating their exits to the corner in rooms to avoid the formation of FIS effect.

  15. Diesel bus emissions measured in a tunnel study.

    Science.gov (United States)

    Jamriska, Milan; Morawska, Lidia; Thomas, Steven; He, Congrong

    2004-12-15

    The emission factors of a bus fleet consisting of approximately 300 diesel-powered buses were measured in a tunnel study under well-controlled conditions during a 2-d monitoring campaign in Brisbane. Particle number and mass concentration levels of submicrometer particles and PM2.5 were monitored by SMPS and DustTrak instruments at the tunnel's entrance and exit, respectively. Correlation between DustTrak and TEOM response to diesel emissions was assessed, and the DustTrak results were recalculated into TEOM equivalent data. The mean value of the number and mass emission factors was (3.11+/-2.41) x 10(14) particles km(-1) for submicrometer particles and 583+/-451 mg km(-1) for PM2.5 (DustTrak), respectively. TEOM PM2.5 equivalent emission factor was 267+/-207 mg km(-1). The results are in good agreement with the emission factors determined from steady-state dynamometer testing of 12 buses from the same Brisbane City bus fleet. The results indicate that when carefully designed, both approaches, the dynamometer and on-road studies, can provide comparable results, applicable for the assessment of the effect of traffic emissions on airborne particle pollution. A brief overview of emission factors determined from other on-road and dynamometer studies reported in the literature as well as with the regulatory values used for the vehicle emission inventory assessment is presented and compared with the results obtained in this study.

  16. γ-irradiated ribosomes from Micrococcus radiodurans in a cell-free protein synthesizing system

    International Nuclear Information System (INIS)

    Suessmuth, R.; Widmann, A.

    1979-01-01

    γ-irradiation inactivation of isolated ribosomes of Micrococcus radiodurans was studied by examining poly U directed synthesis of polyphenylalanine. Ribosomes of M. radiodurans did not show significant γ-radiation sensitivity up to a dose of approx. 11.6 k Gy. Cells of M. radiodurans take up more magnesium than E. coli cells under the same conditions. The magnesium content of ribosomes of M. radiodurans was 18% higher than that of E.coli ribosomes. A possible relation between Mg 2+ -content and γ-resistance is discussed. (orig.) [de

  17. A Numbers Game: Ribosome Densities, Bacterial Growth, and Antibiotic-Mediated Stasis and Death

    Directory of Open Access Journals (Sweden)

    Bruce R. Levin

    2017-02-01

    Full Text Available We postulate that the inhibition of growth and low rates of mortality of bacteria exposed to ribosome-binding antibiotics deemed bacteriostatic can be attributed almost uniquely to these drugs reducing the number of ribosomes contributing to protein synthesis, i.e., the number of effective ribosomes. We tested this hypothesis with Escherichia coli K-12 MG1655 and constructs that had been deleted for 1 to 6 of the 7 rRNA (rrn operons. In the absence of antibiotics, constructs with fewer rrn operons have lower maximum growth rates and longer lag phases than those with more ribosomal operons. In the presence of the ribosome-binding “bacteriostatic” antibiotics tetracycline, chloramphenicol, and azithromycin, E. coli strains with 1 and 2 rrn operons are killed at a substantially higher rate than those with more rrn operons. This increase in the susceptibility of E. coli with fewer rrn operons to killing by ribosome-targeting bacteriostatic antibiotics is not reflected in their greater sensitivity to killing by the bactericidal antibiotic ciprofloxacin, which does not target ribosomes, but also to killing by gentamicin, which does. Finally, when such strains are exposed to these ribosome-targeting bacteriostatic antibiotics, the time before these bacteria start to grow again when the drugs are removed, referred to as the post-antibiotic effect (PAE, is markedly greater for constructs with fewer rrn operons than for those with more rrn operons. We interpret the results of these other experiments reported here as support for the hypothesis that the reduction in the effective number of ribosomes due to binding to these structures provides a sufficient explanation for the action of bacteriostatic antibiotics that target these structures.

  18. Remodeling of ribosomal genes in somatic cells by Xenopus egg extract

    DEFF Research Database (Denmark)

    Østrup, Olga; Hyttel, Poul; Klærke, Dan Arne

    2011-01-01

    Extracts from Xenopus eggs can reprogram gene expression in somatic nuclei, however little is known about the earliest processes associated with the switch in the transcriptional program. We show here that an early reprogramming event is the remodeling of ribosomal chromatin and gene expression....... This occurs within hours of extract treatment and is distinct from a stress response. Egg extract elicits remodeling of the nuclear envelope, chromatin and nucleolus. Nucleolar remodeling involves a rapid and stable decrease in ribosomal gene transcription, and promoter targeting of the nucleolar remodeling...... and elicits a stress-type nuclear response. Thus, an early event of Xenopus egg extract-mediated nuclear reprogramming is the remodeling of ribosomal genes involving nucleolar remodeling complex. Condition-specific and rapid silencing of ribosomal genes may serve as a sensitive marker for evaluation...

  19. Application of an entry-exit tariff model to the gas transport system in Spain

    International Nuclear Information System (INIS)

    Alonso, Alejandro; Serrano, Miguel; Olmos, Luis

    2010-01-01

    Under an entry-exit gas tariff system, reservation of capacity is split into entry capacity, to transport gas from the injection points to a virtual balancing point, and exit capacity, to transport gas from the balancing point to the exit points in the system. Entry-exit tariff for gas transport systems have been recommended by the 3rd EU Energy Package, since they are cost reflective, facilitate gas trade and can provide signals for the location of gas injections or off-takes. The advisability of applying an entry-exit tariff system is discussed in this paper. Apart from this, authors propose an entry-exit tariff model and apply it to compute charges for the Spanish gas transport system in 2009. Results produced by the model are presented as coefficients which should multiply the current postal transport tariff. The paper concludes that entry-exit tariffs would be useful location signals which would result in a better use of the gas transport system in Spain. In those cases where demand exceeds available capacity, as it occurs at the congested connection with France, entry-exit tariffs could be supplemented by capacity charges at entry points resulting from auctions. (author)

  20. The use of the exit interview to reduce turnover amongst healthcare professionals.

    Science.gov (United States)

    Flint, Anndrea; Webster, Joan

    2011-01-19

    Exit interviews are widely used in healthcare organisations to identify reasons for staff attrition, yet their usefulness in limiting turnover is unclear. To determine the effectiveness of various exit interview strategies in decreasing turnover rates amongst healthcare professionals. We used a comprehensive search strategy including an electronic search of the following databases: DARE, CENTRAL, MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC (search date: 7 September 2010) and EPOC Specialised Register (search date: 30 September 2009). We also screened the reference lists of included studies and relevant reviews. Randomised controlled trials, controlled clinical trials, controlled before and after studies and interrupted time series studies comparing turnover rates between healthcare professionals who had undergone one form of exit interview with another form of exit interview or with no interview. Two review authors independently assessed trial quality and extracted data. The search identified 1560 citations of which we considered 19 potentially relevant. The two authors independently reviewed the abstracts of these studies and retrieved the full texts of eight studies. We excluded all eight following independent assessment. They were either interviews, commentaries on how to do an exit interview or descriptive studies about reasons for leaving. We found no trials that matched our inclusion criteria. Evidence about the effectiveness of exit interviews to reduce turnover is currently not available. However, exit interviews may provide useful information about the work environment which, in turn, may be useful in the development of interventions to reduce turnover.

  1. Results of Differential Treatment of Tenckhoff Catheter Exit Site/Tunnel Infection during Peritoneal Dialysis in Patients with End-Stage Chronic Kidney Disease

    OpenAIRE

    V.H. Mishalov; Ye.S. Zavodovskyi; S.M. Hoida; L.Yu. Markulan; I.L. Kuchma

    2015-01-01

    Introduction. Tenckhoff catheter exit site infection (ESI) occurs in 0.05–1.05 cases per patient per year and is a risk factor of termination of peritoneal dialysis (PD). Objective of the work. To evaluate the efficacy of differentiated treatment for ESI in the three-year prospective comparative study. Materials and me-thods. We have examined and treated 141 patients receiving renal replacement therapy by PD. In comparison group (group C) (73 patients) treatment and prevention of ESI was carr...

  2. Exploring the Relationship of Exit Flow and Jam Density in Panic Scenarios Using Animal Dynamics

    NARCIS (Netherlands)

    Sobhani, A.; Sarvi, M.; Duives, D.C.; Ejtemai, O.; Aghabayk, K.; Hoogendoorn, S.P.

    2014-01-01

    There are few studies investigating crowd dynamics in panic situations. They used measures such as exit flow rate to explore the exit performance in evacuation scenarios. However, there is limited research exploring the relationship of exit flow rate and density behind the exit for panic scenarios.

  3. Studies on the catalytic rate constant of ribosomal peptidyltransferase.

    Science.gov (United States)

    Synetos, D; Coutsogeorgopoulos, C

    1987-02-20

    A detailed kinetic analysis of a model reaction for the ribosomal peptidyltransferase is described, using fMet-tRNA or Ac-Phe-tRNA as the peptidyl donor and puromycin as the acceptor. The initiation complex (fMet-tRNA X AUG X 70 S ribosome) or (Ac-Phe-tRNA X poly(U) X 70 S ribosome) (complex C) is isolated and then reacted with excess puromycin (S) to give fMet-puromycin or Ac-Phe-puromycin. This reaction (puromycin reaction) is first order at all concentrations of S tested. An important asset of this kinetic analysis is the fact that the relationship between the first order rate constant kobs and [S] shows hyperbolic saturation and that the value of kobs at saturating [S] is a measure of the catalytic rate constant (k cat) of peptidyltransferase in the puromycin reaction. With fMet-tRNA as the donor, this kcat of peptidyltransferase is 8.3 min-1 when the 0.5 M NH4Cl ribosomal wash is present, compared to 3.8 min-1 in its absence. The kcat of peptidyltransferase is 2.0 min-1 when Ac-Phe-tRNA replaces fMet-tRNA in the presence of the ribosomal wash and decreases to 0.8 min-1 in its absence. This kinetic procedure is the best method available for evaluating changes in the activity of peptidyltransferase in vitro. The results suggest that peptidyltransferase is subjected to activation by the binding of fMet-tRNA to the 70 S initiation complex.

  4. Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Hussmann

    2015-12-01

    Full Text Available Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics.

  5. Linezolid-Dependent Function and Structure Adaptation of Ribosomes in a Staphylococcus epidermidis Strain Exhibiting Linezolid Dependence

    Science.gov (United States)

    Kokkori, Sofia; Apostolidi, Maria; Tsakris, Athanassios; Pournaras, Spyros

    2014-01-01

    Linezolid-dependent growth was recently reported in Staphylococcus epidermidis clinical strains carrying mutations associated with linezolid resistance. To investigate this unexpected behavior at the molecular level, we isolated active ribosomes from one of the linezolid-dependent strains and we compared them with ribosomes isolated from a wild-type strain. Both strains were grown in the absence and presence of linezolid. Detailed biochemical and structural analyses revealed essential differences in the function and structure of isolated ribosomes which were assembled in the presence of linezolid. The catalytic activity of peptidyltransferase was found to be significantly higher in the ribosomes derived from the linezolid-dependent strain. Interestingly, the same ribosomes exhibited an abnormal ribosomal subunit dissociation profile on a sucrose gradient in the absence of linezolid, but the profile was restored after treatment of the ribosomes with an excess of the antibiotic. Our study suggests that linezolid most likely modified the ribosomal assembly procedure, leading to a new functional ribosomal population active only in the presence of linezolid. Therefore, the higher growth rate of the partially linezolid-dependent strains could be attributed to the functional and structural adaptations of ribosomes to linezolid. PMID:24890589

  6. The ribosome uses two active mechanisms to unwind messenger RNA during translation.

    Science.gov (United States)

    Qu, Xiaohui; Wen, Jin-Der; Lancaster, Laura; Noller, Harry F; Bustamante, Carlos; Tinoco, Ignacio

    2011-07-06

    The ribosome translates the genetic information encoded in messenger RNA into protein. Folded structures in the coding region of an mRNA represent a kinetic barrier that lowers the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA at its entry site to allow translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation, such as programmed frameshifting, the modulation of protein expression levels, ribosome localization and co-translational protein folding. Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases, its mechanism is still unknown. Here, using a single-molecule optical tweezers assay on mRNA hairpins, we find that the translation rate of identical codons at the decoding centre is greatly influenced by the GC content of folded structures at the mRNA entry site. Furthermore, force applied to the ends of the hairpin to favour its unfolding significantly speeds translation. Quantitative analysis of the force dependence of its helicase activity reveals that the ribosome, unlike previously studied helicases, uses two distinct active mechanisms to unwind mRNA structure: it destabilizes the helical junction at the mRNA entry site by biasing its thermal fluctuations towards the open state, increasing the probability of the ribosome translocating unhindered; and it mechanically pulls apart the mRNA single strands of the closed junction during the conformational changes that accompany ribosome translocation. The second of these mechanisms ensures a minimal basal rate of translation in the cell; specialized, mechanically stable structures are required to stall the ribosome temporarily. Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs. ©2011 Macmillan Publishers Limited. All rights reserved

  7. Further characterization of ribosome binding to thylakoid membranes

    International Nuclear Information System (INIS)

    Hurewitz, J.; Jagendorf, A.T.

    1987-01-01

    Previous work indicated more polysomes bound to pea (Pisum sativum cv Progress No. 9) thylakoids in light than in the dark, in vivo. With isolated intact chloroplasts incubated in darkness, addition of MgATP had no effect but 24 to 74% more RNA was thylakoid-bound at pH 8.3 than at pH 7. Thus, the major effect of light on ribosome-binding in vivo may be due to higher stroma pH. In isolated pea chloroplasts, initiation inhibitors (pactamycin and kanamycin) decreased the extent of RNA binding, and elongation inhibitors (lincomycin and streptomycin) increased it. Thus, cycling of ribosomes is controlled by translation, initiation, and termination. Bound RNA accounted for 19 to 24% of the total chloroplast RNA and the incorporation of [ 3 H]leucine into thylakoids was proportional to the amount of this bound RNA. These data support the concept that stroma ribosomes are recruited into thylakoid polysomes, which are active in synthesizing thylakoid proteins

  8. Structure of Vibrio cholerae ribosome hibernation promoting factor

    International Nuclear Information System (INIS)

    De Bari, Heather; Berry, Edward A.

    2013-01-01

    The X-ray crystal structure of ribosome hibernation promoting factor from V. cholerae has been determined at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt. The X-ray crystal structure of ribosome hibernation promoting factor (HPF) from Vibrio cholerae is presented at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt. The asymmetric unit contained two molecules of HPF linked by four Co atoms. The metal-binding sites observed in the crystal are probably not related to biological function. The structure of HPF has a typical β–α–β–β–β–α fold consistent with previous structures of YfiA and HPF from Escherichia coli. Comparison of the new structure with that of HPF from E. coli bound to the Thermus thermophilus ribosome [Polikanov et al. (2012 ▶), Science, 336, 915–918] shows that no significant structural changes are induced in HPF by binding

  9. Tunnel magnetoresistance in asymmetric double-barrier magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Useinov, N.Kh.; Petukhov, D.A.; Tagirov, L.R.

    2015-01-01

    The spin-polarized tunnel conductance and tunnel magnetoresistance (TMR) through a planar asymmetric double-barrier magnetic tunnel junction (DBMTJ) have been calculated using quasi-classical model. In DBMTJ nanostructure the magnetization of middle ferromagnetic metal layer can be aligned parallel or antiparallel with respect to the fixed magnetizations of the top and bottom ferromagnetic electrodes. The transmission coefficients of an electron to pass through the barriers have been calculated in terms of quantum mechanics. The dependencies of tunnel conductance and TMR on the applied voltage have been calculated in case of non-resonant transmission. Estimated in the framework of our model, the difference between the spin-channels conductances at low voltages was found relatively large. This gives rise to very high magnitude of TMR. - Highlights: • The spin-polarized conductance through the junction is calculated. • Dependencies of the tunnel conductance vs applied bias are shown. • Bias voltage dependence of tunnel magnetoresistance for the structure is shown

  10. The N-terminal sequence of ribosomal protein L10 from the archaebacterium Halobacterium marismortui and its relationship to eubacterial protein L6 and other ribosomal proteins.

    Science.gov (United States)

    Dijk, J; van den Broek, R; Nasiulas, G; Beck, A; Reinhardt, R; Wittmann-Liebold, B

    1987-08-01

    The amino-terminal sequence of ribosomal protein L10 from Halobacterium marismortui has been determined up to residue 54, using both a liquid- and a gas-phase sequenator. The two sequences are in good agreement. The protein is clearly homologous to protein HcuL10 from the related strain Halobacterium cutirubrum. Furthermore, a weaker but distinct homology to ribosomal protein L6 from Escherichia coli and Bacillus stearothermophilus can be detected. In addition to 7 identical amino acids in the first 36 residues in all four sequences a number of conservative replacements occurs, of mainly hydrophobic amino acids. In this common region the pattern of conserved amino acids suggests the presence of a beta-alpha fold as it occurs in ribosomal proteins L12 and L30. Furthermore, several potential cases of homology to other ribosomal components of the three ur-kingdoms have been found.

  11. Ribosomes: Ribozymes that Survived Evolution Pressures but Is Paralyzed by Tiny Antibiotics

    Science.gov (United States)

    Yonath, Ada

    An impressive number of crystal structures of ribosomes, the universal cellular machines that translate the genetic code into proteins, emerged during the last decade. The determination of ribosome high resolution structure, which was widely considered formidable, led to novel insights into the ribosomal function, namely, fidelity, catalytic mechanism, and polymerize activities. They also led to suggestions concerning its origin and shed light on the action, selectivity and synergism of ribosomal antibiotics; illuminated mechanisms acquiring bacterial resistance and provided structural information for drug improvement and design. These studies required the pioneering and implementation of advanced technologies, which directly influenced the remarkable increase of the number of structures deposited in the Protein Data Bank.

  12. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation.

    Science.gov (United States)

    Wasserman, Michael R; Alejo, Jose L; Altman, Roger B; Blanchard, Scott C

    2016-04-01

    Directional translocation of the ribosome through the mRNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of tRNA and mRNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations revealed direct evidence of structurally and kinetically distinct late intermediates during substrate movement, whose resolution determines the rate of translocation. These steps involve intramolecular events within the EF-G-GDP-bound ribosome, including exaggerated, reversible fluctuations of the small-subunit head domain, which ultimately facilitate peptidyl-tRNA's movement into its final post-translocation position.

  13. International Competition and Small-Firm Exit in US Manufacturing

    OpenAIRE

    Robert M Feinberg

    2013-01-01

    This study analyzes both the determinants of small firm exit rates in US manufacturing over the 1989–2004 period, especially the reaction of domestic firms to the nature of foreign competition as measured by industry-specific real exchange rate movements (interacted with import penetration by industry). These international pressures seem to lead to increased rates of smallest-firm exit in manufacturing, though the magnitudes of these effects are smaller than sometimes discussed. However, high...

  14. Purification and properties of a ribosomal casein kinase from rabbit reticulocytes

    DEFF Research Database (Denmark)

    Issinger, O G

    1977-01-01

    A casein kinase was isolated and purifed from rabbit reticulocytes. About 90% of the enzyme activity co-sedimented with the ribosomal fraction, whereas about 10% of the enzyme activity was found in the ribosome-free supernatant. Both casein kinases (the ribosome-bound enzyme as well as the free...... suggested that the casein kinase is a dimer composed of subunits of identical molecular weight. The enzyme utilizes GTP as well as ATP as a phosphoryl donor. It preferentially phosphorylates acidic proteins, in particular the model substrates casein and phosvitin. Casein kinase is cyclic AMP...

  15. Simulation and analysis of single-ribosome translation

    International Nuclear Information System (INIS)

    Tinoco, Ignacio Jr; Wen, Jin-Der

    2009-01-01

    In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation

  16. Improved social force model based on exit selection for microscopic pedestrian simulation in subway station

    Institute of Scientific and Technical Information of China (English)

    郑勋; 李海鹰; 孟令云; 许心越; 陈旭

    2015-01-01

    An improved social force model based on exit selection is proposed to simulate pedestrians’ microscopic behaviors in subway station. The modification lies in considering three factors of spatial distance, occupant density and exit width. In addition, the problem of pedestrians selecting exit frequently is solved as follows: not changing to other exits in the affected area of one exit, using the probability of remaining preceding exit and invoking function of exit selection after several simulation steps. Pedestrians in subway station have some special characteristics, such as explicit destinations, different familiarities with subway station. Finally, Beijing Zoo Subway Station is taken as an example and the feasibility of the model results is verified through the comparison of the actual data and simulation data. The simulation results show that the improved model can depict the microscopic behaviors of pedestrians in subway station.

  17. Water uptake by and movement through a Backfilled KBS-3V deposition tunnel: results of large-scale simulations

    International Nuclear Information System (INIS)

    Dixon, D.A.; Ramqvist, G.; Jonsson, E.; Gunnarsson, D.; Hansen, J.

    2010-01-01

    Document available in extended abstract form only. Posiva and SKB initiated a joint programme BACLO (Backfilling and Closure of the Deep repository) in 2003 with the aim to develop methods and clay-based materials for backfilling the deposition tunnels of a repository utilizing the KBS-3V deposition concept. This paper summarises the results obtained in intermediate and large-scale simulations to evaluate water movement into and through backfill consisting of bentonite pellets and pre-compacted clay blocks. The main objectives of Baclo Phase III were related to examining backfill materials, deposition concepts and their importance to the clay-block and pellet backfilling concept. Bench-scale studies produced a large body of information on how various processes (e.g. water inflow, piping, erosion, self-healing, homogenisation and interaction between backfill and buffer), might affect the hydro-mechanical evolution of backfill components. The tests described in this paper examined the movement of water into and through assemblies of clay blocks and bentonite pellets/granules and represent a substantial up-scaling and inclusion of parameters that more closely simulate a field situation. In total, 27 intermediate-scale tests have been completed and 18 large-scale tests (∼ 1/2-tunnel cross-section) will be completed at SKB's Aespoe HRL by mid 2010. At intermediate-scale, point inflow rates ranging from 0.01 to 1.0 l/min were applied to block - dry pellet assemblies and water movement into and through the system was monitored. Tests determined that it is critical to provide clay blocks with lateral support and confinement as quickly as possible following block installation. Exposure of the blocks to even low rates of water ingress can result in rapid loss of block cohesion and subsequent slumping of the block materials into the spaces between the blocks and the tunnel walls. Installation of granular or pelletized bentonite clay between the blocks and the walls

  18. Does Business Cycle Have an Impact on Entrants and Exits?

    Directory of Open Access Journals (Sweden)

    Nikolay Sterev

    2017-03-01

    Full Text Available Purpose: The role of entrants and exits has enlarged indisputably over recent years. The basic explanation is connected to the deepening of innovation's influence on industrial growth. Furthermore, new businesses have to be more effective, and based on products, technological or organizational innovations, and exits have to be ineffective (respectively unprofitable, based on denoted products or technology. Design/methodology/approach: According to the above-mentioned prerequisites, policymakers need to manage the role (respectively the impact that entrants (new start-up companies and exits play in industrial growth. Nevertheless, this impact is not a cornerstone of the Bulgarian National Strategy, or the Europe 2020 Strategy. Findings: The paper tries to answer the following two questions: 1 Do new start-up companies and exits have any role and influence on economic growth in Bulgaria? and 2 Does the role (respectively the impact of entrants and exits in industrial growth change according to economic cycle? Research limitations/implications: In addition, according to the Lisbon Strategy, as well as the European Union's (EU Strategy 2020, the current economic policy supports entrepreneurship and innovations. Thus, the establishment of innovative companies, as well as the development of innovative, incumbent business are core issues of EU economic policy for the past decade. Originality/value: The paper builds on the industrial dynamic methodology and on the understanding of how business decisions (entrepreneurship, innovations, and R&D on micro level correspond to macro level (GDP growth and innovation policy.

  19. Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA

    Science.gov (United States)

    Andreeva, Irena

    2018-01-01

    During translation, consecutive ribosomes load on an mRNA and form a polysome. The first ribosome binds to a single-stranded mRNA region and moves toward the start codon, unwinding potential mRNA structures on the way. In contrast, the following ribosomes can dock at the start codon only when the first ribosome has vacated the initiation site. Here we show that loading of the second ribosome on a natural 38-nt-long 5′ untranslated region of lpp mRNA, which codes for the outer membrane lipoprotein from Escherichia coli, takes place before the leading ribosome has moved away from the start codon. The rapid formation of this standby complex depends on the presence of ribosomal proteins S1/S2 in the leading ribosome. The early recruitment of the second ribosome to the standby site before translation by the leading ribosome and the tight coupling between translation elongation by the first ribosome and the accommodation of the second ribosome can contribute to high translational efficiency of the lpp mRNA. PMID:29632209

  20. The comparison of exit-site care with normal saline and povidone-iodine in preventing exit-site infection and peritonitis in children on chronic peritoneal dialysis treatment

    Directory of Open Access Journals (Sweden)

    Onder Yavascan

    2011-01-01

    Full Text Available Peritonitis and catheter exit- site infections (ESI are important causes of hospitalization and catheter loss in patients undergoing chronic peritoneal dialysis (CPD. The frequency of infection can be reduced by scrupulous exit- site care with or without topical antiseptics. There are no studies showing any benefit in the use of povidone-iodine or normal saline for care of exit- sites in long- term CPD patients. In this study, we aimed to determine the potential effectiveness of the application of povidone-iodine or normal saline at the catheter exit- site in preventing ESI and peritonitis in children on CPD. A total of 98 patients treated with either povidone-iodine or normal saline were included in this study. Group I (34 patients used povidone-iodine and group II (64 patients simply cleansed the exit- site with normal saline (0.9% NaCl. Dressings were changed 2 to 3 times in a week. The total cumulative follow- up time was 3233 patient- months. ESIs occurred in 10 (29.4% of 34 patients using povidone-iodine and in 10 (15.6% of 64 patients using normal saline. The frequency of ESI was significantly high in group I (povidone-iodine patients. The mean rate of ESI was 1 episode/60.8 patient- months for group I versus 1 episode/144 patient- months for group II (P 0.05. In conclusion, exit- site care with normal saline is an effective strategy in reducing the incidence of ESI in children on CPD. It can thus significantly reduce morbidity, catheter loss, and the need to transfer patients on peritoneal dialysis to hemodialysis.

  1. Influence of drill helical direction on exit damage development in drilling carbon fiber reinforced plastic

    Science.gov (United States)

    Bai, Y.; Jia, Z. Y.; Wang, F. J.; Fu, R.; Guo, H. B.; Cheng, D.; Zhang, B. Y.

    2017-06-01

    Drilling is inevitable for CFRP components’ assembling process in the aviation industry. The exit damage frequently occurs and affects the load carrying capacity of components. Consequently, it is of great urgency to enhance drilling exit quality on CFRP components. The article aims to guide the reasonable choice of drill helical direction and effectively reduce exit damage. Exit observation experiments are carried out with left-hand helical, right-hand helical and straight one-shot drill drilling T800S CFRP laminates separately. The development rules of exit damage and delamination factor curves are obtained. Combined with loading conditions and fracture modes of push-out burrs, and thrust force curves, the influence of drill helical direction on exit damage development is derived. It is found that the main fracture modes for left-hand helical, right-hand helical, and straight one-shot drill are mode I, extrusive fracture, mode III respectively. Among them, mode III has the least effect on exit damage development. Meanwhile, the changing rate of thrust force is relative slow for right-hand helical and straight one-shot drill in the thrust force increasing phase of stage II, which is disadvantaged for exit damage development. Therefore, straight one-shot drill’s exit quality is the best.

  2. Magnetic tunnel junctions with monolayer hexagonal boron nitride tunnel barriers

    Energy Technology Data Exchange (ETDEWEB)

    Piquemal-Banci, M.; Galceran, R.; Bouzehouane, K.; Anane, A.; Petroff, F.; Fert, A.; Dlubak, B.; Seneor, P. [Unité Mixte de Physique, CNRS, Thales, Univ. Paris-Sud, Université Paris-Saclay, Palaiseau 91767 (France); Caneva, S.; Martin, M.-B.; Weatherup, R. S.; Kidambi, P. R.; Robertson, J.; Hofmann, S. [Department of Engineering, University of Cambridge, Cambridge CB21PZ (United Kingdom); Xavier, S. [Thales Research and Technology, 1 avenue Augustin Fresnel, Palaiseau 91767 (France)

    2016-03-07

    We report on the integration of atomically thin 2D insulating hexagonal boron nitride (h-BN) tunnel barriers into Co/h-BN/Fe magnetic tunnel junctions (MTJs). The h-BN monolayer is directly grown by chemical vapor deposition on Fe. The Conductive Tip Atomic Force Microscopy (CT-AFM) measurements reveal the homogeneity of the tunnel behavior of our h-BN layers. As expected for tunneling, the resistance depends exponentially on the number of h-BN layers. The h-BN monolayer properties are also characterized through integration into complete MTJ devices. A Tunnel Magnetoresistance of up to 6% is observed for a MTJ based on a single atomically thin h-BN layer.

  3. 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.

  4. Variability in ACL tunnel placement: observational clinical study of surgeon ACL tunnel variability.

    Science.gov (United States)

    Wolf, Brian R; Ramme, Austin J; Wright, Rick W; Brophy, Robert H; McCarty, Eric C; Vidal, Armando R; Parker, Richard D; Andrish, Jack T; Amendola, Annunziato

    2013-06-01

    Multicenter and multisurgeon cohort studies on anterior cruciate ligament (ACL) reconstruction are becoming more common. Minimal information exists on intersurgeon and intrasurgeon variability in ACL tunnel placement. Purpose/ The purpose of this study was to analyze intersurgeon and intrasurgeon variability in ACL tunnel placement in a series of The Multicenter Orthopaedic Outcomes Network (MOON) ACL reconstruction patients and in a clinical cohort of ACL reconstruction patients. The hypothesis was that there would be minimal variability between surgeons in ACL tunnel placement. Cross-sectional study; Level of evidence, 3. Seventy-eight patients who underwent ACL reconstruction by 8 surgeons had postoperative imaging with computed tomography, and ACL tunnel location and angulation were analyzed using 3-dimensional surface processing and measurement. Intersurgeon and intrasurgeon variability in ACL tunnel placement was analyzed. For intersurgeon variability, the range in mean ACL femoral tunnel depth between surgeons was 22%. For femoral tunnel height, there was a 19% range. Tibial tunnel location from anterior to posterior on the plateau had a 16% range in mean results. There was only a small range of 4% for mean tibial tunnel location from the medial to lateral dimension. For intrasurgeon variability, femoral tunnel depth demonstrated the largest ranges, and tibial tunnel location from medial to lateral on the plateau demonstrated the least variability. Overall, surgeons were relatively consistent within their own cases. Using applied measurement criteria, 85% of femoral tunnels and 90% of tibial tunnels fell within applied literature-based guidelines. Ninety-one percent of the axes of the femoral tunnels fell within the boundaries of the femoral footprint. The data demonstrate that surgeons performing ACL reconstructions are relatively consistent between each other. There is, however, variability of average tunnel placement up to 22% of mean condylar depth

  5. Interaction between groundwater and TBM (Tunnel Boring Machine) excavated tunnels

    OpenAIRE

    Font Capó, Jordi

    2012-01-01

    A number of problems, e.g. sudden inflows are encountered during tunneling under the piezometric level, especially when the excavation crosses high transmissivity areas. These inflows may drag materials when the tunnel crosses low competent layers, resulting in subsidence, chimney formation and collapses. Moreover, inflows can lead to a decrease in head level because of aquifer drainage. Tunnels can be drilled by a tunnel boring machine (TBM) to minimize inflows and groundwater impacts, restr...

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

    Science.gov (United States)

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

    2016-01-01

    Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides whose members target proteases with potent reversible inhibition. The product structure is constructed by three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here, we describe the detailed structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases, MdnC and MdnB, interact with a conserved α-helix of the precursor peptide using a novel precursor peptide recognition mechanism. The results provide insight into the unique protein/protein interactions key to the chemistry, suggest an origin of the natural combinatorial synthesis of microviridin peptides and provide a framework for future engineering efforts to generate designed compounds. PMID:27669417

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

    Science.gov (United States)

    Li, Kunhua; Condurso, Heather L; Li, Gengnan; Ding, Yousong; Bruner, Steven D

    2016-11-01

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

  8. Epigenetics as a First Exit Problem

    Science.gov (United States)

    Aurell, E.; Sneppen, K.

    2002-01-01

    We develop a framework to discuss the stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the λ prophage. The formalism defines a quantitative measure of robustness of inherited states.

  9. Organization of proteins in mammalian mitochondrial ribosomes: accessibility to lactoperoxidase-catalyzed radioiodination

    International Nuclear Information System (INIS)

    Denslow, N.D.; O'Brien, T.W.

    1984-01-01

    To assess the relative exposure of individual ribosomal proteins (r-proteins) in the large and small subunits of the bovine mitochondrial ribosome, double label iodination technique was used. Regions of r-proteins exposed in purified ribosomal subunits were labeled with 131 I using the lactoperoxidase-catalyzed iodination system, and additional reactive groups available upon denaturing the r-proteins in urea were labeled with 125 I using the chloramine-T mediated reaction. The ratio of 131 I to 125 I incorporated into individual proteins under these conditions is representative of the degree of exposure for each of the proteins in the subunits. In this manner, the r-proteins have been grouped into 3 classes depending on their degree of exposure: high exposure, intermediate exposure, and essentially buried. While both subunits have a few proteins in the highly exposed group, and a large number of proteins in the intermediate exposure group, only the large ribosomal subunit has an appreciable number of proteins which appear essentially buried. The more buried proteins may serve mainly structural roles, perhaps acting as assembly proteins, since many from this group bind to ribosomal RNA. The more superficially disposed proteins may comprise binding sites for macromolecules that interact with ribosomes during protein synthesis, as well as stabilizing the association of the large and small subribosomal particles

  10. Evaluation of six TPS algorithms in computing entrance and exit doses

    Science.gov (United States)

    Metwaly, Mohamed; Glegg, Martin; Baggarley, Shaun P.; Elliott, Alex

    2014-01-01

    Entrance and exit doses are commonly measured in in vivo dosimetry for comparison with expected values, usually generated by the treatment planning system (TPS), to verify accuracy of treatment delivery. This report aims to evaluate the accuracy of six TPS algorithms in computing entrance and exit doses for a 6 MV beam. The algorithms tested were: pencil beam convolution (Eclipse PBC), analytical anisotropic algorithm (Eclipse AAA), AcurosXB (Eclipse AXB), FFT convolution (XiO Convolution), multigrid superposition (XiO Superposition), and Monte Carlo photon (Monaco MC). Measurements with ionization chamber (IC) and diode detector in water phantoms were used as a reference. Comparisons were done in terms of central axis point dose, 1D relative profiles, and 2D absolute gamma analysis. Entrance doses computed by all TPS algorithms agreed to within 2% of the measured values. Exit doses computed by XiO Convolution, XiO Superposition, Eclipse AXB, and Monaco MC agreed with the IC measured doses to within 2%‐3%. Meanwhile, Eclipse PBC and Eclipse AAA computed exit doses were higher than the IC measured doses by up to 5.3% and 4.8%, respectively. Both algorithms assume that full backscatter exists even at the exit level, leading to an overestimation of exit doses. Despite good agreements at the central axis for Eclipse AXB and Monaco MC, 1D relative comparisons showed profiles mismatched at depths beyond 11.5 cm. Overall, the 2D absolute gamma (3%/3 mm) pass rates were better for Monaco MC, while Eclipse AXB failed mostly at the outer 20% of the field area. The findings of this study serve as a useful baseline for the implementation of entrance and exit in vivo dosimetry in clinical departments utilizing any of these six common TPS algorithms for reference comparison. PACS numbers: 87.55.‐x, 87.55.D‐, 87.55.N‐, 87.53.Bn PMID:24892349

  11. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  12. After exit: Academic achievement patterns of former English language learners.

    Directory of Open Access Journals (Sweden)

    Ester J. de Jong

    2004-09-01

    Full Text Available With few exceptions, accountability systems for programs for English language learners (ELLs have focused on the achievement patterns of ELLs who are still considered “limited English proficient” and program evaluations have been unable to answer the question whether ELLs actually catch up with English proficient peers after attending a bilingual or English as a Second Language (ESL program. Disaggregating data for former ELLs can therefore provide important information for long-term district and program accountability. The study was concerned with the achievement patterns in English language arts, Math, and Science of former ELLs who attended a bilingual and a English as a Second Language (ESL program. It also explored whether length of program participation and grade level exited played a significant role in predicting academic achievement patterns for these exited students. Results indicate that 4th grade students more closely paralleled non- ELL students’ achievement patterns than 8th grade students, particularly for the BE students. While length of program participation is not a significant predictor of former ELLs’ academic success, exit grade does emerge as an important variable to take into consideration in setting exit guidelines.

  13. Frequency driven inversion of tunnel magnetoimpedance and observation of positive tunnel magnetocapacitance in magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Parui, Subir; Ribeiro, Mário; Atxabal, Ainhoa; Llopis, Roger; Bedoya-Pinto, Amilcar; Sun, Xiangnan; Casanova, Fèlix; Hueso, Luis E.

    2016-01-01

    The relevance for modern computation of non-volatile high-frequency memories makes ac-transport measurements of magnetic tunnel junctions (MTJs) crucial for exploring this regime. Here, we demonstrate a frequency-mediated effect in which the tunnel magnetoimpedance reverses its sign in a classical Co/Al 2 O 3 /NiFe MTJ, whereas we only observe a gradual decrease in the tunnel magnetophase. Such effects are explained by the capacitive coupling of a parallel resistor and capacitor in the equivalent circuit model of the MTJ. Furthermore, we report a positive tunnel magnetocapacitance effect, suggesting the presence of a spin-capacitance at the two ferromagnet/tunnel-barrier interfaces. Our results are important for understanding spin transport phenomena at the high frequency regime in which the spin-polarized charge accumulation due to spin-dependent penetration depth at the two interfaces plays a crucial role.

  14. Frequency driven inversion of tunnel magnetoimpedance and observation of positive tunnel magnetocapacitance in magnetic tunnel junctions

    Energy Technology Data Exchange (ETDEWEB)

    Parui, Subir, E-mail: s.parui@nanogune.eu, E-mail: l.hueso@nanogune.eu; Ribeiro, Mário; Atxabal, Ainhoa; Llopis, Roger [CIC nanoGUNE, 20018 Donostia-San Sebastian (Spain); Bedoya-Pinto, Amilcar [CIC nanoGUNE, 20018 Donostia-San Sebastian (Spain); Max Planck Institute of Microstructure Physics, D-06120 Halle (Germany); Sun, Xiangnan [CIC nanoGUNE, 20018 Donostia-San Sebastian (Spain); National Center for Nanoscience and Technology, 100190 Beijing (China); Casanova, Fèlix; Hueso, Luis E., E-mail: s.parui@nanogune.eu, E-mail: l.hueso@nanogune.eu [CIC nanoGUNE, 20018 Donostia-San Sebastian (Spain); IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain)

    2016-08-01

    The relevance for modern computation of non-volatile high-frequency memories makes ac-transport measurements of magnetic tunnel junctions (MTJs) crucial for exploring this regime. Here, we demonstrate a frequency-mediated effect in which the tunnel magnetoimpedance reverses its sign in a classical Co/Al{sub 2}O{sub 3}/NiFe MTJ, whereas we only observe a gradual decrease in the tunnel magnetophase. Such effects are explained by the capacitive coupling of a parallel resistor and capacitor in the equivalent circuit model of the MTJ. Furthermore, we report a positive tunnel magnetocapacitance effect, suggesting the presence of a spin-capacitance at the two ferromagnet/tunnel-barrier interfaces. Our results are important for understanding spin transport phenomena at the high frequency regime in which the spin-polarized charge accumulation due to spin-dependent penetration depth at the two interfaces plays a crucial role.

  15. Drink Specials and the Intoxication Levels of Patrons Exiting College Bars

    Science.gov (United States)

    Thombs, Dennis L.; Dodd, Virginia; Porkorny, Steven B.; Omli, Morrow R.; O'Mara, Ryan; Webb, Monica C.; Lacaci, Diana M.; Werch, Chad

    2008-01-01

    Objectives: To determine whether drink specials independently increase patrons' risk of achieving a high level of intoxication upon exiting drinking establishments. Methods: In a campus community, data were collected from exiting patrons (N=291) via sidewalk interviews and breath tests on 6 nights of 2 consecutive semesters. Results: A…

  16. Carpal Tunnel Syndrome

    Science.gov (United States)

    ... a passing cramp? It could be carpal tunnel syndrome. The carpal tunnel is a narrow passageway of ... three times more likely to have carpal tunnel syndrome than men. Early diagnosis and treatment are important ...

  17. Mutations in ribosomal protein L3 and 23S ribosomal RNA at the peptidyl transferase centre are associated with reduced susceptibility to tiamulin in Brachyspira spp. isolates.

    Science.gov (United States)

    Pringle, Märit; Poehlsgaard, Jacob; Vester, Birte; Long, Katherine S

    2004-12-01

    The pleuromutilin antibiotic tiamulin binds to the ribosomal peptidyl transferase centre. Three groups of Brachyspira spp. isolates with reduced tiamulin susceptibility were analysed to define resistance mechanisms to the drug. Mutations were identified in genes encoding ribosomal protein L3 and 23S rRNA at positions proximal to the peptidyl transferase centre. In two groups of laboratory-selected mutants, mutations were found at nucleotide positions 2032, 2055, 2447, 2499, 2504 and 2572 of 23S rRNA (Escherichia coli numbering) and at amino acid positions 148 and 149 of ribosomal protein L3 (Brachyspira pilosicoli numbering). In a third group of clinical B. hyodysenteriae isolates, only a single mutation at amino acid 148 of ribosomal protein L3 was detected. Chemical footprinting experiments show a reduced binding of tiamulin to ribosomal subunits from mutants with decreased susceptibility to the drug. This reduction in drug binding is likely the resistance mechanism for these strains. Hence, the identified mutations located near the tiamulin binding site are predicted to be responsible for the resistance phenotype. The positions of the mutated residues relative to the bound drug advocate a model where the mutations affect tiamulin binding indirectly through perturbation of nucleotide U2504.

  18. Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

    Directory of Open Access Journals (Sweden)

    Nicholas T. Ingolia

    2014-09-01

    Full Text Available Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5′ UTRs and long noncoding RNAs (lncRNAs. Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs. Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences.

  19. Theory of superconducting tunneling without the tunneling Hamiltonian

    International Nuclear Information System (INIS)

    Arnold, G.B.

    1987-01-01

    When a tunneling barrier is nearly transparent, the standard tunneling (or transfer) Hamiltonian approximation fails. The author describes the theory which is necessary for calculating the tunneling current in these cases, and illustrate it by comparing theory and experiment on superconductor/insulator/superconductor (SIS) junctions have ultra-thin tunnel barriers. This theory accurately explains the subgap structure which appears in the dynamical resistance of such SIS junctions, including many observed details which no previous theory has reproduced. The expression for the current through an SIS junction with an ultrathin barrier is given by I(t) = Re{Sigma/sub n/ J/sub n/ (omega/sub o/)e/sup in omega/o/sup t/} where omega/sub o/ = 2eV/h is the Josephson frequency, V is the bias voltage, and the J/sub n/ are voltage dependent coefficients, one for each positive or negative integer, n, and n=0. The relative sign of the terms involving cos(n omega/sub o/t) and sin(n omega/sub o/t) agrees with experiment, in contrast to previous theories of Josephson tunneling

  20. 14 CFR 135.129 - Exit seating.

    Science.gov (United States)

    2010-01-01

    ... emergency evacuation provided by the certificate holder in printed or graphic form or the ability to... accordance with this section. (d) Each certificate holder shall include on passenger information cards.... (e) Each certificate holder shall include on passenger information cards, at each exit seat— (1) In...

  1. Ribosome slowed by mutation to streptomycin resistance. [Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Galas, D J; Branscomb, E W

    1976-08-12

    The effect of mutation to streptomycin resistance on the speed of polypeptide elongation in Escherichia coli was investigated. Translation speed was determined by measuring the time required for the first newly synthesized ..beta..-galactosidase molecules to appear after induction of the lactose operon. The results showed that ribosome speed is not a fixed parameter inherent to the protein synthetic apparatus, but a variable determined by the kinetics of translation and ultimately by the structure of the ribosome. (HLW)

  2. Ribosomal stress induces L11- and p53-dependent apoptosis in mouse pluripotent stem cells.

    Science.gov (United States)

    Morgado-Palacin, Lucia; Llanos, Susana; Serrano, Manuel

    2012-02-01

    Ribosome biogenesis is the most demanding energetic process in proliferating cells and it is emerging as a critical sensor of cellular homeostasis. Upon disturbance of ribosome biogenesis, specific free ribosomal proteins, most notably L11, bind and inhibit Mdm2, resulting in activation of the tumor suppressor p53. This pathway has been characterized in somatic and cancer cells, but its function in embryonic pluripotent cells has remained unexplored. Here, we show that treatment with low doses of Actinomycin D or depletion of ribosomal protein L37, two well-established inducers of ribosomal stress, activate p53 in an L11-dependent manner in mouse embryonic stem cells (ESCs) and in induced pluripotent stem cells (iPSCs). Activation of p53 results in transcriptional induction of p53 targets, including p21, Mdm2, Pidd, Puma, Noxa and Bax. Finally, ribosomal stress elicits L11- and p53-dependent apoptosis in ESCs/iPSCs. These results extend to pluripotent cells the functionality of the ribosomal stress pathway and we speculate that this could be a relevant cellular checkpoint during early embryogenesis.

  3. ABC-F Proteins Mediate Antibiotic Resistance through Ribosomal Protection.

    Science.gov (United States)

    Sharkey, Liam K R; Edwards, Thomas A; O'Neill, Alex J

    2016-03-22

    Members of the ABC-F subfamily of ATP-binding cassette proteins mediate resistance to a broad array of clinically important antibiotic classes that target the ribosome of Gram-positive pathogens. The mechanism by which these proteins act has been a subject of long-standing controversy, with two competing hypotheses each having gained considerable support: antibiotic efflux versus ribosomal protection. Here, we report on studies employing a combination of bacteriological and biochemical techniques to unravel the mechanism of resistance of these proteins, and provide several lines of evidence that together offer clear support to the ribosomal protection hypothesis. Of particular note, we show that addition of purified ABC-F proteins to anin vitrotranslation assay prompts dose-dependent rescue of translation, and demonstrate that such proteins are capable of displacing antibiotic from the ribosomein vitro To our knowledge, these experiments constitute the first direct evidence that ABC-F proteins mediate antibiotic resistance through ribosomal protection.IMPORTANCEAntimicrobial resistance ranks among the greatest threats currently facing human health. Elucidation of the mechanisms by which microorganisms resist the effect of antibiotics is central to understanding the biology of this phenomenon and has the potential to inform the development of new drugs capable of blocking or circumventing resistance. Members of the ABC-F family, which includelsa(A),msr(A),optr(A), andvga(A), collectively yield resistance to a broader range of clinically significant antibiotic classes than any other family of resistance determinants, although their mechanism of action has been controversial since their discovery 25 years ago. Here we present the first direct evidence that proteins of the ABC-F family act to protect the bacterial ribosome from antibiotic-mediated inhibition. Copyright © 2016 Sharkey et al.

  4. Door locking and exit security measures on acute psychiatric admission wards

    NARCIS (Netherlands)

    Nijman, H.L.I.; Bowers, L.; Haglund, K.; Muir-Cochrane, E.; Simpson, A.; Merwe, M. van der

    2011-01-01

    Locking the exit doors of psychiatric wards is believed to reduce the risk of patients absconding. The aims of the study were to investigate both the prevalence of door locking and other exit security measures on UK admission wards, as well as whether door locking appears to be effective in keeping

  5. Fluctuations in protein synthesis from a single RNA template: stochastic kinetics of ribosomes.

    Science.gov (United States)

    Garai, Ashok; Chowdhury, Debashish; Ramakrishnan, T V

    2009-01-01

    Proteins are polymerized by cyclic machines called ribosomes, which use their messenger RNA (mRNA) track also as the corresponding template, and the process is called translation. We explore, in depth and detail, the stochastic nature of the translation. We compute various distributions associated with the translation process; one of them--namely, the dwell time distribution--has been measured in recent single-ribosome experiments. The form of the distribution, which fits best with our simulation data, is consistent with that extracted from the experimental data. For our computations, we use a model that captures both the mechanochemistry of each individual ribosome and their steric interactions. We also demonstrate the effects of the sequence inhomogeneities of real genes on the fluctuations and noise in translation. Finally, inspired by recent advances in the experimental techniques of manipulating single ribosomes, we make theoretical predictions on the force-velocity relation for individual ribosomes. In principle, all our predictions can be tested by carrying out in vitro experiments.

  6. Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

    Science.gov (United States)

    Kimura, M; Kimura, J; Hatakeyama, T

    1988-11-21

    The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

  7. EXIT Chart Analysis of Binary Message-Passing Decoders

    DEFF Research Database (Denmark)

    Lechner, Gottfried; Pedersen, Troels; Kramer, Gerhard

    2007-01-01

    Binary message-passing decoders for LDPC codes are analyzed using EXIT charts. For the analysis, the variable node decoder performs all computations in the L-value domain. For the special case of a hard decision channel, this leads to the well know Gallager B algorithm, while the analysis can...... be extended to channels with larger output alphabets. By increasing the output alphabet from hard decisions to four symbols, a gain of more than 1.0 dB is achieved using optimized codes. For this code optimization, the mixing property of EXIT functions has to be modified to the case of binary message......-passing decoders....

  8. Tunneling works. Tunnel koji

    Energy Technology Data Exchange (ETDEWEB)

    Higo, M [Hazam Gumi, Ltd., Tokyo (Japan)

    1991-10-25

    A mountain tunneling method for rock-beds used to be applied mainly to construction works in the mountains under few restrictions by environmental problems. However, construction works near residential sreas have been increasing. There are such enviromental problems due to tunneling works as vibration, noise, lowering of ground-water level, and influences on other structures. This report mainly describes the measurement examples of vibration and noise accompanied with blasting and the effects of the measures to lessen such influences. When the tunneling works for the railroad was carried out on the natural ground mainly composed of basalt, vibration of the test blasting was measured at three stations with piezoelectric accelerometers. Then, ordinary blasting, mutistage blasting, and ABM blasting methods were used properly besed on the above results, and only a few complaints were made. In the different works, normal noise and low-frequency sound were mesured at 22 stations around the pit mouth. As countermeasures for noise, sound-proof sheets, walls, and single and double doors were installed and foundto be effective. 1 ref., 6 figs., 1 tab.

  9. Predicting The Exit Time Of Employees In An Organization Using Statistical Model

    Directory of Open Access Journals (Sweden)

    Ahmed Al Kuwaiti

    2015-08-01

    Full Text Available Employees are considered as an asset to any organization and each organization provide a better and flexible working environment to retain its best and resourceful workforce. As such continuous efforts are being taken to avoid or extend the exitwithdrawal of employees from the organization. Human resource managers are facing a challenge to predict the exit time of employees and there is no precise model existing at present in the literature. This study has been conducted to predict the probability of exit of an employee in an organization using appropriate statistical model. Accordingly authors designed a model using Additive Weibull distribution to predict the expected exit time of employee in an organization. In addition a Shock model approach is also executed to check how well the Additive Weibull distribution suits in an organization. The analytical results showed that when the inter-arrival time increases the expected time for the employees to exit also increases. This study concluded that Additive Weibull distribution can be considered as an alternative in the place of Shock model approach to predict the exit time of employee in an organization.

  10. 14 CFR 121.585 - Exit seating.

    Science.gov (United States)

    2010-01-01

    ... section and related to emergency evacuation provided by the certificate holder in printed or graphic form... include on passenger information cards, presented in the language in which briefings and oral commands are... passenger information cards, at each exit seat— (1) In the primary language in which emergency commands are...

  11. The ribosome-associated complex antagonizes prion formation in yeast.

    Science.gov (United States)

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

    2015-01-01

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

  12. Protein folding on the ribosome studied using NMR spectroscopy

    Science.gov (United States)

    Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

    2013-01-01

    NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

  13. The subcellular distribution of the human ribosomal "stalk" components: P1, P2 and P0 proteins

    DEFF Research Database (Denmark)

    Tchórzewski, Marek; Krokowski, Dawid; Rzeski, Wojciech

    2003-01-01

    The ribosomal "stalk" structure is a distinct lateral protuberance located on the large ribosomal subunit in prokaryotic, as well as in eukaryotic cells. In eukaryotes, this ribosomal structure is composed of the acidic ribosomal P proteins, forming two hetero-dimers (P1/P2) attached...

  14. Aggregating job exit statuses of a plurality of compute nodes executing a parallel application

    Science.gov (United States)

    Aho, Michael E.; Attinella, John E.; Gooding, Thomas M.; Mundy, Michael B.

    2015-07-21

    Aggregating job exit statuses of a plurality of compute nodes executing a parallel application, including: identifying a subset of compute nodes in the parallel computer to execute the parallel application; selecting one compute node in the subset of compute nodes in the parallel computer as a job leader compute node; initiating execution of the parallel application on the subset of compute nodes; receiving an exit status from each compute node in the subset of compute nodes, where the exit status for each compute node includes information describing execution of some portion of the parallel application by the compute node; aggregating each exit status from each compute node in the subset of compute nodes; and sending an aggregated exit status for the subset of compute nodes in the parallel computer.

  15. sORFs.org: a repository of small ORFs identified by ribosome profiling.

    Science.gov (United States)

    Olexiouk, Volodimir; Crappé, Jeroen; Verbruggen, Steven; Verhegen, Kenneth; Martens, Lennart; Menschaert, Gerben

    2016-01-04

    With the advent of ribosome profiling, a next generation sequencing technique providing a "snap-shot'' of translated mRNA in a cell, many short open reading frames (sORFs) with ribosomal activity were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these 'sORFs', indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Comparison of exit time moment spectra for extrinsic metric balls

    DEFF Research Database (Denmark)

    Hurtado, Ana; Markvorsen, Steen; Palmer, Vicente

    2012-01-01

    We prove explicit upper and lower bounds for the $L^1$-moment spectra for the Brownian motion exit time from extrinsic metric balls of submanifolds $P^m$ in ambient Riemannian spaces $N^n$. We assume that $P$ and $N$ both have controlled radial curvatures (mean curvature and sectional curvature...... obtain new intrinsic comparison results for the exit time spectra for metric balls in the ambient manifolds $N^n$ themselves....

  17. The importance of ribosome production, and the 5S RNP-MDM2 pathway, in health and disease.

    Science.gov (United States)

    Pelava, Andria; Schneider, Claudia; Watkins, Nicholas J

    2016-08-15

    Ribosomes are abundant, large RNA-protein complexes that are the source of all protein synthesis in the cell. The production of ribosomes is an extremely energetically expensive cellular process that has long been linked to human health and disease. More recently, it has been shown that ribosome biogenesis is intimately linked to multiple cellular signalling pathways and that defects in ribosome production can lead to a wide variety of human diseases. Furthermore, changes in ribosome production in response to nutrient levels in the diet lead to metabolic re-programming of the liver. Reduced or abnormal ribosome production in response to cellular stress or mutations in genes encoding factors critical for ribosome biogenesis causes the activation of the tumour suppressor p53, which leads to re-programming of cellular transcription. The ribosomal assembly intermediate 5S RNP (ribonucleoprotein particle), containing RPL5, RPL11 and the 5S rRNA, accumulates when ribosome biogenesis is blocked. The excess 5S RNP binds to murine double minute 2 (MDM2), the main p53-suppressor in the cell, inhibiting its function and leading to p53 activation. Here, we discuss the involvement of ribosome biogenesis in the homoeostasis of p53 in the cell and in human health and disease. © 2016 The Author(s).

  18. Tunneling junction as an open system. Normal tunneling

    International Nuclear Information System (INIS)

    Ono, Y.

    1978-01-01

    The method of the tunneling Hamiltonian is reformulated in the case of normal tunneling by introducing two independent particle baths. Due to the baths, it becomes possible to realize a final stationary state where the electron numbers of the two electrodes in the tunneling system are maintained constant and where there exists a stationary current. The effect of the bath-system couplings on the current-voltage characteristics of the junction is discussed in relation to the usual expression of the current as a function of voltage. (Auth.)

  19. Formal procedures of the exit from a community for a university social media agency

    OpenAIRE

    Peleschyshyn, Andriy; Peleschyshyn, Oksana; Korzh, Roman

    2016-01-01

    The aim of the paper is to consider the process of exiting of a university from an online community. The importance of performing the task of exiting in a proper way is proved. Preconditions and risks of the process are investigated. All the stages of the suggested algorithm for exiting from online community are scrutinized.

  20. The nuclear import of ribosomal proteins is regulated by mTOR

    Science.gov (United States)

    Kazyken, Dubek; Kaz, Yelimbek; Kiyan, Vladimir; Zhylkibayev, Assylbek A.; Chen, Chien-Hung; Agarwal, Nitin K.; Sarbassov, Dos D.

    2014-01-01

    Mechanistic target of rapamycin (mTOR) is a central component of the essential signaling pathway that regulates cell growth and proliferation by controlling anabolic processes in cells. mTOR exists in two distinct mTOR complexes known as mTORC1 and mTORC2 that reside mostly in cytoplasm. In our study, the biochemical characterization of mTOR led to discovery of its novel localization on nuclear envelope where it associates with a critical regulator of nuclear import Ran Binding Protein 2 (RanBP2). We show that association of mTOR with RanBP2 is dependent on the mTOR kinase activity that regulates the nuclear import of ribosomal proteins. The mTOR kinase inhibitors within thirty minutes caused a substantial decrease of ribosomal proteins in the nuclear but not cytoplasmic fraction. Detection of a nuclear accumulation of the GFP-tagged ribosomal protein rpL7a also indicated its dependence on the mTOR kinase activity. The nuclear abundance of ribosomal proteins was not affected by inhibition of mTOR Complex 1 (mTORC1) by rapamycin or deficiency of mTORC2, suggesting a distinctive role of the nuclear envelope mTOR complex in the nuclear import. Thus, we identified that mTOR in association with RanBP2 mediates the active nuclear import of ribosomal proteins. PMID:25294810

  1. Efficiency, Leverage and Exit: The Role of Information Asymmetry in Concentrated Industries

    DEFF Research Database (Denmark)

    Siyahhan, Baran

    2011-01-01

    This paper develops a real options model of imperfect competition with asymmetric information that analyzes firms’ exit decisions. Optimal exit decision is linked to firm characteristics such as financial leverage and efficiency. The model shows that informational asymmetries can lead more...

  2. Efficiency, Leverage and Exit: The Role of Information Asymmetry in Concentrated Industries

    DEFF Research Database (Denmark)

    Siyahhan, Baran

    This paper develops a real options model of imperfect competition with asymmetric information that analyzes firms’ exit decisions. Optimal exit decision is linked to firm characteristics such as financial leverage and efficiency. The model shows that informational asymmetries can lead more...

  3. 5SRNAdb: an information resource for 5S ribosomal RNAs.

    Science.gov (United States)

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

    2016-01-04

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

  4. Quantum theory of tunneling

    CERN Document Server

    Razavy, Mohsen

    2014-01-01

    In this revised and expanded edition, in addition to a comprehensible introduction to the theoretical foundations of quantum tunneling based on different methods of formulating and solving tunneling problems, different semiclassical approximations for multidimensional systems are presented. Particular attention is given to the tunneling of composite systems, with examples taken from molecular tunneling and also from nuclear reactions. The interesting and puzzling features of tunneling times are given extensive coverage, and the possibility of measurement of these times with quantum clocks are critically examined. In addition by considering the analogy between evanescent waves in waveguides and in quantum tunneling, the times related to electromagnetic wave propagation have been used to explain certain aspects of quantum tunneling times. These topics are treated in both non-relativistic as well as relativistic regimes. Finally, a large number of examples of tunneling in atomic, molecular, condensed matter and ...

  5. The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6.

    Science.gov (United States)

    Dobrenel, Thomas; Mancera-Martínez, Eder; Forzani, Céline; Azzopardi, Marianne; Davanture, Marlène; Moreau, Manon; Schepetilnikov, Mikhail; Chicher, Johana; Langella, Olivier; Zivy, Michel; Robaglia, Christophe; Ryabova, Lyubov A; Hanson, Johannes; Meyer, Christian

    2016-01-01

    Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.

  6. Toward 3D structural information from quantitative electron exit wave analysis

    International Nuclear Information System (INIS)

    Borisenko, Konstantin B; Moldovan, Grigore; Kirkland, Angus I; Wang, Amy; Van Dyck, Dirk; Chen, Fu-Rong

    2012-01-01

    Simulations show that using a new direct imaging detector and accurate exit wave restoration algorithms allows nearly quantitative restoration of electron exit wave phase, which can be regarded as only qualitative for conventional indirect imaging cameras. This opens up a possibility of extracting accurate information on 3D atomic structure of the sample even from a single projection.

  7. Translation activity of chimeric ribosomes composed of Escherichia coli and Bacillus subtilis or Geobacillus stearothermophilus subunits

    Directory of Open Access Journals (Sweden)

    Sayaka Tsuji

    2017-07-01

    Full Text Available Ribosome composition, consisting of rRNA and ribosomal proteins, is highly conserved among a broad range of organisms. However, biochemical studies focusing on ribosomal subunit exchangeability between organisms remain limited. In this study, we show that chimeric ribosomes, composed of Escherichia coli and Bacillus subtilis or E. coli and Geobacillus stearothermophilus subunits, are active for β-galactosidase translation in a highly purified E. coli translation system. Activities of the chimeric ribosomes showed only a modest decrease when using E. coli 30 S subunits, indicating functional conservation of the 50 S subunit between these bacterial species.

  8. Human nucleolus organizers on nonhomologous chromosomes can share the same ribosomal gene variants.

    Science.gov (United States)

    Krystal, M; D'Eustachio, P; Ruddle, F H; Arnheim, N

    1981-01-01

    The distributions of three human ribosomal gene polymorphisms among individual chromosomes containing nucleolus organizers were analyzed by using mouse--human hybrid cells. Different nucleolus organizers can contain the same variant, suggesting the occurrence of genetic exchanges among ribosomal gene clusters on nonhomologous chromosomes. Such exchanges appear to occur less frequently in mice. This difference is discussed in terms of the nucleolar organization and chromosomal location of ribosomal gene clusters in humans and mice. Images PMID:6272316

  9. Multi-perspective smFRET reveals rate-determining late intermediates of ribosomal translocation

    Science.gov (United States)

    Wasserman, Michael R.; Alejo, Jose L.; Altman, Roger B.; Blanchard, Scott C.

    2016-01-01

    Directional translocation of the ribosome through the messenger RNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of transfer and messenger RNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we have tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations reveal direct evidence of structurally and kinetically distinct, late intermediates during substrate movement, whose resolution is rate-determining to the translocation mechanism. These steps involve intra-molecular events within the EFG(GDP)-bound ribosome, including exaggerated, reversible fluctuations of the small subunit head domain, which ultimately facilitate peptidyl-tRNA’s movement into its final post-translocation position. PMID:26926435

  10. Site-specific fluorescent labeling of nascent proteins on the translating ribosome.

    Science.gov (United States)

    Saraogi, Ishu; Zhang, Dawei; Chandrasekaran, Sandhya; Shan, Shu-ou

    2011-09-28

    As newly synthesized proteins emerge from the ribosome, they interact with a variety of cotranslational cellular machineries that facilitate their proper folding, maturation, and localization. These interactions are essential for proper function of the cell, and the ability to study these events is crucial to understanding cellular protein biogenesis. To this end, we have developed a highly efficient method to generate ribosome-nascent chain complexes (RNCs) site-specifically labeled with a fluorescent dye on the nascent polypeptide. The fluorescent RNC provides real-time, quantitative information on its cotranslational interaction with the signal recognition particle and will be a valuable tool in elucidating the role of the translating ribosome in numerous biochemical pathways.

  11. Thermus Thermophilus as a Model System for the Study of Ribosomal Antibiotic Resistance

    Science.gov (United States)

    Gregory, Steven T.

    2018-03-01

    Ribosomes are the intracellular ribonucleoprotein machines responsible for the translation of mRNA sequence into protein sequence. As an essential cell component, the ribosome is the target of numerous antibiotics that bind to critical functional sites to impair protein synthesis. Mutations causing resistance to antibiotics arise in antibiotic binding sites, and an understanding of the basis of resistance will be an essential component of efforts to develop new antibiotics by rational drug design. We have identified a number of antibiotic-resistance mutations in ribosomal genes of the thermophilic bacterium Thermus thermophilus. This species offers two primary advantages for examining the structural basis of antibiotic-resistance, in particular, its potential for genetic manipulation and the suitability of its ribosomes for analysis by X-ray crystallography. Mutations we have identified in this organism are in many instances identical to those found in other bacterial species, including important pathogens, a result of the extreme conservation of ribosome functional sites. Here I summarize the advantages of this organism as a model system to study antibiotic-resistance mechanisms at the molecular level.

  12. Spin-dependent tunnelling in magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Tsymbal, Evgeny Y; Mryasov, Oleg N; LeClair, Patrick R

    2003-01-01

    The phenomenon of electron tunnelling has been known since the advent of quantum mechanics, but continues to enrich our understanding of many fields of physics, as well as creating sub-fields on its own. Spin-dependent tunnelling (SDT) in magnetic tunnel junctions (MTJs) has recently aroused enormous interest and has developed in a vigorous field of research. The large tunnelling magnetoresistance (TMR) observed in MTJs garnered much attention due to possible applications in non-volatile random-access memories and next-generation magnetic field sensors. This led to a number of fundamental questions regarding the phenomenon of SDT. In this review article we present an overview of this field of research. We discuss various factors that control the spin polarization and magnetoresistance in MTJs. Starting from early experiments on SDT and their interpretation, we consider thereafter recent experiments and models which highlight the role of the electronic structure of the ferromagnets, the insulating layer, and the ferromagnet/insulator interfaces. We also discuss the role of disorder in the barrier and in the ferromagnetic electrodes and their influence on TMR. (topical review)

  13. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress.

    Science.gov (United States)

    Sloan, Katherine E; Bohnsack, Markus T; Watkins, Nicholas J

    2013-10-17

    Several proto-oncogenes and tumor suppressors regulate the production of ribosomes. Ribosome biogenesis is a major consumer of cellular energy, and defects result in p53 activation via repression of mouse double minute 2 (MDM2) homolog by the ribosomal proteins RPL5 and RPL11. Here, we report that RPL5 and RPL11 regulate p53 from the context of a ribosomal subcomplex, the 5S ribonucleoprotein particle (RNP). We provide evidence that the third component of this complex, the 5S rRNA, is critical for p53 regulation. In addition, we show that the 5S RNP is essential for the activation of p53 by p14(ARF), a protein that is activated by oncogene overexpression. Our data show that the abundance of the 5S RNP, and therefore p53 levels, is determined by factors regulating 5S complex formation and ribosome integration, including the tumor suppressor PICT1. The 5S RNP therefore emerges as the critical coordinator of signaling pathways that couple cell proliferation with ribosome production. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  14. rRNA maturation in yeast cells depleted of large ribosomal subunit proteins.

    Directory of Open Access Journals (Sweden)

    Gisela Pöll

    Full Text Available The structural constituents of the large eukaryotic ribosomal subunit are 3 ribosomal RNAs, namely the 25S, 5.8S and 5S rRNA and about 46 ribosomal proteins (r-proteins. They assemble and mature in a highly dynamic process that involves more than 150 proteins and 70 small RNAs. Ribosome biogenesis starts in the nucleolus, continues in the nucleoplasm and is completed after nucleo-cytoplasmic translocation of the subunits in the cytoplasm. In this work we created 26 yeast strains, each of which conditionally expresses one of the large ribosomal subunit (LSU proteins. In vivo depletion of the analysed LSU r-proteins was lethal and led to destabilisation and degradation of the LSU and/or its precursors. Detailed steady state and metabolic pulse labelling analyses of rRNA precursors in these mutant strains showed that LSU r-proteins can be grouped according to their requirement for efficient progression of different steps of large ribosomal subunit maturation. Comparative analyses of the observed phenotypes and the nature of r-protein-rRNA interactions as predicted by current atomic LSU structure models led us to discuss working hypotheses on i how individual r-proteins control the productive processing of the major 5' end of 5.8S rRNA precursors by exonucleases Rat1p and Xrn1p, and ii the nature of structural characteristics of nascent LSUs that are required for cytoplasmic accumulation of nascent subunits but are nonessential for most of the nuclear LSU pre-rRNA processing events.

  15. Association Between Health Plan Exit From Medicaid Managed Care and Quality of Care, 2006-2014.

    Science.gov (United States)

    Ndumele, Chima D; Schpero, William L; Schlesinger, Mark J; Trivedi, Amal N

    2017-06-27

    State Medicaid programs have increasingly contracted with insurers to provide medical care services for enrollees (Medicaid managed care plans). Insurers that provide these plans can exit Medicaid programs each year, with unclear effects on quality of care and health care experiences. To determine the frequency and interstate variation of health plan exit from Medicaid managed care and evaluate the relationship between health plan exit and market-level quality. Retrospective cohort of all comprehensive Medicaid managed care plans (N = 390) during the interval 2006-2014. Plan exit, defined as the withdrawal of a managed care plan from a state's Medicaid program. Eight measures from the Healthcare Effectiveness Data and Information Set were used to construct 3 composite indicators of quality (preventive care, chronic disease care management, and maternity care). Four measures from the Consumer Assessment of Healthcare Providers and Systems were combined into a composite indicator of patient experience, reflecting the proportion of beneficiaries rating experiences as 8 or above on a 0-to-10-point scale. Outcome data were available for 248 plans (68% of plans operating prior to 2014, representing 78% of beneficiaries). Of the 366 comprehensive Medicaid managed care plans operating prior to 2014, 106 exited Medicaid. These exiting plans enrolled 4 848 310 Medicaid beneficiaries, with a mean of 606 039 beneficiaries affected by plan exits annually. Six states had a mean of greater than 10% of Medicaid managed care recipients enrolled in plans that exited, whereas 10 states experienced no plan exits. Plans that exited from a state's Medicaid market performed significantly worse prior to exiting than those that remained in terms of preventive care (57.5% vs 60.4%; difference, 2.9% [95% CI, 0.3% to 5.5%]), maternity care (69.7% vs 73.6%; difference, 3.8% [95% CI, 1.7% to 6.0%]), and patient experience (73.5% vs 74.8%; difference, 1.3% [95% CI, 0.6% to 1

  16. Stor forskel på kommuners bande-exit

    DEFF Research Database (Denmark)

    Mørck, Line Lerche

    2015-01-01

    DEBAT: Kommunerne har meget forskellige exit-tilbud til bande- og rockermedlemmer. Der er brug for mere indgående forskning, så vi ved, hvad der virker bedst, skriver Line Lerche Mørck, lektor i pædagogisk psykologi....

  17. Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes.

    Science.gov (United States)

    Erales, Jenny; Marchand, Virginie; Panthu, Baptiste; Gillot, Sandra; Belin, Stéphane; Ghayad, Sandra E; Garcia, Maxime; Laforêts, Florian; Marcel, Virginie; Baudin-Baillieu, Agnès; Bertin, Pierre; Couté, Yohann; Adrait, Annie; Meyer, Mélanie; Therizols, Gabriel; Yusupov, Marat; Namy, Olivier; Ohlmann, Théophile; Motorin, Yuri; Catez, Frédéric; Diaz, Jean-Jacques

    2017-12-05

    Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.

  18. Management Optimization of the Luminous Flux Regulation of a Lighting System in Road Tunnels. A First Approach to the Exertion of Predictive Control Systems

    Directory of Open Access Journals (Sweden)

    Ferdinando Salata

    2016-10-01

    Full Text Available Lighting very long road tunnels implies a high consumption of electrical energy since it requires a proper illumination during the whole day. In particular, in the daytime, the illuminance levels right at the tunnel entrance threshold and exit zones must be higher than those characterizing the inside of the tunnel; in this way, the eye of the driver is able to adapt and be safe while passing from a high natural illumination of the outside to the lighting conditions characterizing the inside of the tunnel. However this causes a high energy demand. Therefore, this case study investigates whether it is possible to minimize the energy demand through the exertion of an automatic new control system regulating the luminous fluxes of artificial sources (guaranteeing the parameters set by the regulation with respect to the variation of the natural light characterizing the outside. The innovative control systems must be characterized by high reliability levels in order to guarantee conditions which are not dangerous to the driver if an outage occurs and minimize their maintenance costs. To carry out this type of study, the software DIALux was used to simulate a tunnel with a dimming system (with lamps characterized by a high luminous efficiency regulated by a pre-programmed logic control system (with high Mean Time Between Failure (MTBF values. The savings obtained enabled the amortization of the solution here suggested in a time interval that makes it an advantageous choice economically speaking.

  19. 14 CFR 23.805 - Flightcrew emergency exits.

    Science.gov (United States)

    2010-01-01

    ... emergency exit must be located to allow rapid evacuation of the crew and have a size and shape of at least a... than six feet from the ground, an assisting means must be provided. The assisting means may be a rope...

  20. Exit Polling in an Emergent Democracy: The Complex Case of Ukraine

    Directory of Open Access Journals (Sweden)

    Natalya Nikolaevna Kharchenko

    2010-05-01

    Full Text Available This report considers the methodological specifics of conducting exit polls to verify election returns, mainly using an example of election campaigns in Ukraine from 2002-2007. The deepest public resonance was aroused by exit polls conducted after the second round of Ukrainian presidential elections in 2004. These polls were one of the factors, which led to massive demonstrations (the so-called "Orange Revolution" and the revocation of election results. The authors show that in the environment of administrative pressure on voters, governmental control of mass media, and severe political struggle, inaccuracy increases. Thus, to acquire reliable and valid information, the polling methods used must be modified. The recommendations given for the methodology of conducting exit polls may be useful for emergent democratic countries.

  1. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

    Science.gov (United States)

    Irigoyen, Nerea; Firth, Andrew E; Jones, Joshua D; Chung, Betty Y-W; Siddell, Stuart G; Brierley, Ian

    2016-02-01

    Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal

  2. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

    Directory of Open Access Journals (Sweden)

    Nerea Irigoyen

    2016-02-01

    Full Text Available Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV, are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59, a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the

  3. 5S Ribosomal RNA Is an Essential Component of a Nascent Ribosomal Precursor Complex that Regulates the Hdm2-p53 Checkpoint

    Directory of Open Access Journals (Sweden)

    Giulio Donati

    2013-07-01

    Full Text Available Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted.

  4. 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint.

    Science.gov (United States)

    Donati, Giulio; Peddigari, Suresh; Mercer, Carol A; Thomas, George

    2013-07-11

    Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA) and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Tunnel fire dynamics

    CERN Document Server

    Ingason, Haukur; Lönnermark, Anders

    2015-01-01

    This book covers a wide range of issues in fire safety engineering in tunnels, describes the phenomena related to tunnel fire dynamics, presents state-of-the-art research, and gives detailed solutions to these major issues. Examples for calculations are provided. The aim is to significantly improve the understanding of fire safety engineering in tunnels. Chapters on fuel and ventilation control, combustion products, gas temperatures, heat fluxes, smoke stratification, visibility, tenability, design fire curves, heat release, fire suppression and detection, CFD modeling, and scaling techniques all equip readers to create their own fire safety plans for tunnels. This book should be purchased by any engineer or public official with responsibility for tunnels. It would also be of interest to many fire protection engineers as an application of evolving technical principles of fire safety.

  6. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

    Science.gov (United States)

    Gomez, James E; Kaufmann-Malaga, Benjamin B; Wivagg, Carl N; Kim, Peter B; Silvis, Melanie R; Renedo, Nikolai; Ioerger, Thomas R; Ahmad, Rushdy; Livny, Jonathan; Fishbein, Skye; Sacchettini, James C; Carr, Steven A; Hung, Deborah T

    2017-02-21

    Antibiotic resistance arising via chromosomal mutations is typically specific to a particular antibiotic or class of antibiotics. We have identified mutations in genes encoding ribosomal components in Mycobacterium smegmatis that confer resistance to several structurally and mechanistically unrelated classes of antibiotics and enhance survival following heat shock and membrane stress. These mutations affect ribosome assembly and cause large-scale transcriptomic and proteomic changes, including the downregulation of the catalase KatG, an activating enzyme required for isoniazid sensitivity, and upregulation of WhiB7, a transcription factor involved in innate antibiotic resistance. Importantly, while these ribosomal mutations have a fitness cost in antibiotic-free medium, in a multidrug environment they promote the evolution of high-level, target-based resistance. Further, suppressor mutations can then be easily acquired to restore wild-type growth. Thus, ribosomal mutations can serve as stepping-stones in an evolutionary path leading to the emergence of high-level, multidrug resistance.

  7. Proton tunneling in solids

    Energy Technology Data Exchange (ETDEWEB)

    Kondo, J.

    1998-10-01

    The tunneling rate of the proton and its isotopes between interstitial sites in solids is studied theoretically. The phonons and/or the electrons in the solid have two effects on the tunneling phenomenon. First, they suppress the transfer integral between two neighbouring states. Second, they give rise to a finite lifetime of the proton state. Usually the second effect is large and the tunneling probability per unit time (tunneling rate) can be defined. In some cases, however, a coherent tunneling is expected and actually observed. (author)

  8. Proton tunneling in solids

    International Nuclear Information System (INIS)

    Kondo, J.

    1998-01-01

    The tunneling rate of the proton and its isotopes between interstitial sites in solids is studied theoretically. The phonons and/or the electrons in the solid have two effects on the tunneling phenomenon. First, they suppress the transfer integral between two neighbouring states. Second, they give rise to a finite lifetime of the proton state. Usually the second effect is large and the tunneling probability per unit time (tunneling rate) can be defined. In some cases, however, a coherent tunneling is expected and actually observed. (author)

  9. Biphasic character of ribosomal translocation and non-Michaelis-Menten kinetics of translation

    Science.gov (United States)

    Xie, Ping

    2014-12-01

    We study theoretically the kinetics of mRNA translocation in the wild-type (WT) Escherichia coli ribosome, which is composed of a small 30 S and large 50 S subunit, and the ribosomes with mutations to some intersubunit bridges such as B1a, B4, B7a, and B8. The theoretical results reproduce well the available in vitro experimental data on the biphasic kinetics of the forward mRNA translocation catalyzed by elongation factor G (EF-G) hydrolyzing GTP, which can be best fit by the sum of two exponentials, and the monophasic kinetics of the spontaneous reverse mRNA translocation in the absence of the elongation factor, which can be best fit by a single-exponential function, in both the WT and mutant ribosomes. We show that both the mutation-induced increase in the maximal rate of the slow phase for the forward mRNA translocation and that in the rate of the spontaneous reverse mRNA translocation result from a reduction in the intrinsic energy barrier to resist the rotational movements between the two subunits, giving the same degree of increase in the two rates. The mutation-induced increase in the maximal rate of the fast phase for the forward mRNA translocation results mainly from the increase in the rate of the ribosomal unlocking, a conformational change in the ribosome that widens the mRNA channel for the mRNA translocation to take place, which could be partly due to the effect of the mutation on the intrasubunit 30S head rotation. Moreover, we study the translation rate of the WT and mutant ribosomes. It is shown that the translation rate versus the concentration of EF-G-GTP does not follow the Michaelis-Menten (MM) kinetics, which is in sharp contrast to the general property of other enzymes that the rate of the enzymatic reaction versus the concentration of a substrate follows the MM kinetics. The physical origin of this non-MM kinetics for the ribosome is revealed.

  10. Ribosome evolution: Emergence of peptide synthesis machinery

    Indian Academy of Sciences (India)

    suggested the dynamic movement of ribosomal proteins. The L2 protein (a .... Such kinds of interactions are important in elucidating the evolution of RNA .... Tamura K 2009 Molecular handedness of life: significance of RNA aminoacylation.

  11. Is there a channel in the ribosome for nascent peptide. Labellimg of translating ribosomes with atomar tritium

    Energy Technology Data Exchange (ETDEWEB)

    Kolb, V A; Kammer, A A; Spirin, A S

    1987-01-01

    The method of tritium bombardment was applied to investigate exposure of growing peptide on the surface of ribsome E.coli. Distribution of radioactivity by fractions is presented. Tritium inclusion in all the aminoacid residues of heteropeptide testifies to its exposure on the surface of the ribosome.

  12. A Diversity Exit Interview/Survey for the Military

    National Research Council Canada - National Science Library

    Knouse, Stephen

    2001-01-01

    The exit interview and survey are means for identifying organizational problems, including diversity issues, through individuals separating from the organization, who are in a unique position to supply candid feedback...

  13. Symmetry associated with symmetry break: Revisiting ants and humans escaping from multiple-exit rooms

    Science.gov (United States)

    Ji, Q.; Xin, C.; Tang, S. X.; Huang, J. P.

    2018-02-01

    Crowd panic has incurred massive injuries or deaths throughout the world, and thus understanding it is particularly important. It is now a common knowledge that crowd panic induces "symmetry break" in which some exits are jammed while others are underutilized. Amazingly, here we show, by experiment, simulation and theory, that a class of symmetry patterns come to appear for ants and humans escaping from multiple-exit rooms while the symmetry break exists. Our symmetry pattern is described by the fact that the ratio between the ensemble-averaging numbers of ants or humans escaping from different exits is equal to the ratio between the widths of the exits. The mechanism lies in the effect of heterogeneous preferences of agents with limited information for achieving the Nash equilibrium. This work offers new insights into how to improve public safety because large public areas are always equipped with multiple exits, and it also brings an ensemble-averaging method for seeking symmetry associated with symmetry breaking.

  14. Exits from Temporary Jobs in Europe: A Competing Risks Analysis

    DEFF Research Database (Denmark)

    D'Addio, Anna Christina; Rosholm, Michael

    2005-01-01

    We study transitions out of temporary jobs using the waves 1994-1999 of the European Community Household Panel applying a discrete time duration model. Specifically, we use a multinomial logitmodel distinguishing between exits into permanent employment and non-employment. Two different specificat......We study transitions out of temporary jobs using the waves 1994-1999 of the European Community Household Panel applying a discrete time duration model. Specifically, we use a multinomial logitmodel distinguishing between exits into permanent employment and non-employment. Two different...

  15. Adolescents Exiting Homelessness over Two Years: The Risk Amplification and Abatement Model

    Science.gov (United States)

    Milburn, Norweeta G.; Rice, Eric; Rotheram-Borus, Mary Jane; Mallett, Shelley; Rosenthal, Doreen; Batterham, Phillip; May, Susanne J.; Witkin, Andrea; Duan, Naihua

    2009-01-01

    The Risk Amplification and Abatement Model (RAAM) demonstrates that negative contact with socializing agents amplify risk, while positive contact abates risk for homeless adolescents. To test this model, the likelihood of exiting homelessness and returning to familial housing at 2 years and stably exiting over time are examined with longitudinal…

  16. Fluctuation Dominated Josephson Tunneling with a Scanning Tunneling Microscope

    International Nuclear Information System (INIS)

    Naaman, O.; Teizer, W.; Dynes, R. C.

    2001-01-01

    We demonstrate Josephson tunneling in vacuum tunnel junctions formed between a superconducting scanning tunneling microscope tip and a Pb film, for junction resistances in the range 50--300 k Omega. We show that the superconducting phase dynamics is dominated by thermal fluctuations, and that the Josephson current appears as a peak centered at small finite voltage. In the presence of microwave fields (f=15.0 GHz) the peak decreases in magnitude and shifts to higher voltages with increasing rf power, in agreement with theory

  17. The ISI Tunnel

    Science.gov (United States)

    1993-10-01

    DP /etc/tunnelvisa p zephyr dark -star TCP /etc/tunnelvisa p zephyr dak’star ICMP /etc/tunnelvisa p zephyr quark MDP /etc/tunnelvisa p zephyr quark ...drax-net-yp 128.9.32.2 1 route add quark -net-yp 128.9.32.3 1 route add vlsi-net-yp 128.9.32.4 1 route add darkstar-net-yp 128.9.32.3 1 route add rocky...TCP /etc/tunnel-visa p zephyr quark ICMP /etc/tunnel-visa p zephyr drax tTI)P /etc/tunnel-visa p zephyr drax TCP /etc/tunnel_visa p zephyr drax ICMP

  18. Resonant tunnel magnetoresistance in a double magnetic tunnel junction

    KAUST Repository

    Useinov, Arthur; Useinov, Niazbeck Kh H; Tagirov, Lenar R.; Kosel, Jü rgen

    2011-01-01

    We present quasi-classical approach to calculate a spin-dependent current and tunnel magnetoresistance (TMR) in double magnetic tunnel junctions (DMTJ) FML/I/FMW/I/FMR, where the magnetization of the middle ferromagnetic metal layer FMW can

  19. The 70S ribosome modulates the ATPase activity of Escherichia coli YchF.

    Science.gov (United States)

    Becker, Marion; Gzyl, Katherine E; Altamirano, Alvin M; Vuong, Anthony; Urban, Kirstin; Wieden, Hans-Joachim

    2012-10-01

    YchF is one of two universally conserved GTPases with unknown cellular function. As a first step toward elucidating YchF's cellular role, we performed a detailed biochemical characterization of the protein from Escherichia coli. Our data from fluorescence titrations not only confirmed the surprising finding that YchFE.coli binds adenine nucleotides more efficiently than guanine nucleotides, but also provides the first evidence suggesting that YchF assumes two distinct conformational states (ATP- and ADP-bound) consistent with the functional cycle of a typical GTPase. Based on an in vivo pull-down experiment using a His-tagged variant of YchF from E. coli (YchFE.coli), we were able to isolate a megadalton complex containing the 70S ribosome. Based on this finding, we report the successful reconstitution of a YchF•70S complex in vitro, revealing an affinity (KD) of the YchFE.coli•ADPNP complex for 70S ribosomes of 3 μM. The in vitro reconstitution data also suggests that the identity of the nucleotide-bound state of YchF (ADP or ATP) modulates its affinity for 70S ribosomes. A detailed Michaelis-Menten analysis of YchF's catalytic activity in the presence and the absence of the 70S ribosome and its subunits revealed for the first time that the 70S ribosome is able to stimulate YchF's ATPase activity (~10-fold), confirming the ribosome as part of the functional cycle of YchF. Our findings taken together with previously reported data for the human homolog of YchF (hOLA1) indicate a high level of evolutionary conservation in the enzymatic properties of YchF and suggest that the ribosome is the main functional partner of YchF not only in bacteria.

  20. Transgenic C. elegans dauer larvae expressing hookworm phospho null DAF-16/FoxO exit dauer.

    Directory of Open Access Journals (Sweden)

    Verena Gelmedin

    Full Text Available Parasitic hookworms and the free-living model nematode Caenorhabtidis elegans share a developmental arrested stage, called the dauer stage in C. elegans and the infective third-stage larva (L3 in hookworms. One of the key transcription factors that regulate entrance to and exit from developmental arrest is the forkhead transcription factor DAF-16/FoxO. During the dauer stage, DAF-16 is activated and localized in the nucleus. DAF-16 is negatively regulated by phosphorylation by the upstream kinase AKT, which causes DAF-16 to localize out of the nucleus and the worm to exit from dauer. DAF-16 is conserved in hookworms, and hypothesized to control recovery from L3 arrest during infection. Lacking reverse genetic techniques for use in hookworms, we used C. elegans complementation assays to investigate the function of Ancylostoma caninum DAF-16 during entrance and exit from L3 developmental arrest. We performed dauer switching assays and observed the restoration of the dauer phenotype when Ac-DAF-16 was expressed in temperature-sensitive dauer defective C. elegans daf-2(e1370;daf-16(mu86 mutants. AKT phosphorylation site mutants of Ac-DAF-16 were also able to restore the dauer phenotype, but surprisingly allowed dauer exit when temperatures were lowered. We used fluorescence microscopy to localize DAF-16 during dauer and exit from dauer in C. elegans DAF-16 mutant worms expressing Ac-DAF-16, and found that Ac-DAF-16 exited the nucleus during dauer exit. Surprisingly, Ac-DAF-16 with mutated AKT phosphorylation sites also exited the nucleus during dauer exit. Our results suggest that another mechanism may be involved in the regulation DAF-16 nuclear localization during recovery from developmental arrest.

  1. Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis.

    Science.gov (United States)

    Boehringer, Daniel; O'Farrell, Heather C; Rife, Jason P; Ban, Nenad

    2012-03-23

    The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.

  2. Structural Insights into Methyltransferase KsgA Function in 30S Ribosomal Subunit Biogenesis*

    Science.gov (United States)

    Boehringer, Daniel; O'Farrell, Heather C.; Rife, Jason P.; Ban, Nenad

    2012-01-01

    The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3′-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation. PMID:22308031

  3. Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria.

    Science.gov (United States)

    Glotz, C; Müssig, J; Gewitz, H S; Makowski, I; Arad, T; Yonath, A; Wittmann, H G

    1987-11-01

    Ordered three-dimensional crystals of 70S ribosomes as well as of 30S and 50S ribosomal subunits from various bacteria (E. coli, Bacillus stearothermophilus, Thermus thermophilus and Halobacterium marismortui) have been grown by vapour diffusion in hanging drops using mono- and polyalcohols. A new compact crystal form of 50S subunits has been obtained, and it is suitable for crystallographic studies at medium resolution. In addition, from one crystal form large crystals could be grown in X-ray capillaries. In all cases the crystals were obtained from functionally active ribosomal particles, and the particles from dissolved crystals retained their integrity and biological activity.

  4. Tunneling through landsliding zone; Jisuberi chitainai no tunnel seko

    Energy Technology Data Exchange (ETDEWEB)

    Konbu, A; Hatabu, K; Kano, T [Tekken Corp., Tokyo (Japan)

    1994-08-01

    At the new tunnel construction site of the Shirakata tunnel on the Obama line in Yamaguchi Prefecture, a landsliding occurred at about 60 meters to the upper portion obliquely to the right hand side of the shaft when the excavation progressed to about 10 meters from the starting side. The landslide caused displacement at the shaft opening and change in the supports. As a result of the re-investigation, it was confirmed that the slide face went through the tunnel cross section. The measures taken were removal of the upper soil and an adoption of the all ground fastening (AGF) method (injection type long tip fastening method) as an auxiliary construction to stop loosening of the natural ground associated with the tunnel excavation. The result was a completion of tunneling the landsliding zone without a problem. This paper reports the AGF method adopted in the above construction, together with the construction works and natural ground conditions. The AGF method is about the same as the pipe roof method with regard to the natural ground accepting mechanism and the materials used. The difference is building an improved body in a limited area in the natural ground around the steel pipes by injecting the fixing material. The use of this method caused no problems in subsidence and displacement in the surrounding ground, and completed the tunneling construction without an unusual event. 1 ref., 7 figs., 2 tabs.

  5. Two-dimensional exit dosimetry using a liquid-filled electronic portal imaging device and a convolution model

    International Nuclear Information System (INIS)

    Boellaard, Ronald; Herk, Marcel van; Uiterwaal, Hans; Mijnheer, Ben

    1997-01-01

    Background and purpose: To determine the accuracy of two-dimensional exit dose measurements with an electronic portal imaging device, EPID, using a convolution model for a variety of clinically relevant situations. Materials and methods: Exit doses were derived from portal dose images, obtained with a liquid-filled EPID at distances of 50 cm or more behind the patient, by using a convolution model. The resulting on- and off-axis exit dose values were first compared with ionization chamber exit dose measurements for homogeneous and inhomogeneous phantoms in open and wedged 4,8 and 18 MV photon beams. The accuracy of the EPID exit dose measurements was then determined for a number of anthropomorphic phantoms (lung and larynx) irradiated under clinical conditions and for a few patients treated in an 8 MV beam. The latter results were compared with in vivo exit dose measurements using diodes. Results: The exit dose can be determined from portal images with an accuracy of 1.2% (1 SD) compared with ionization chamber measurements for open beams and homogeneous phantoms at all tested beam qualities. In the presence of wedges and for inhomogeneous phantoms the average relative accuracy slightly deteriorated to 1.7% (1 SD). For lung phantoms in a 4 MV beam a similar accuracy was obtained after refinement of our convolution model, which requires knowledge of the patient contour. Differences between diode and EPID exit dose measurements for an anthropomorphic lung phantom in an 8 MV beam were 2.5% at most, with an average agreement within 1% (1 SD). For larynx phantoms in a 4 MV beam exit doses obtained with an ionization chamber and EPID agreed within 1.5% (1 SD). Finally, exit doses in a few patients irradiated in an 8 MV beam could be determined with the EPID with an accuracy of 1.1% (1 SD) relative to exit dose measurements using diodes. Conclusions: Portal images, obtained with our EPID and analyzed with our convolution model, can be used to determine the exit dose

  6. Explaining discrepancies in reproductive health indicators from population-based surveys and exit surveys: a case from Rwanda.

    Science.gov (United States)

    Meekers, D; Ogada, E A

    2001-06-01

    Reproductive health programmes often need exit surveys and population-based surveys for monitoring and evaluation. This study investigates why such studies produce discrepant estimates of condom use, sexual behaviour and condom brand knowledge, and discusses the implications for future use of exit surveys for programme monitoring. Logistic regression is used to explain differences between a household survey of 1295 persons and an exit survey among a random sample of 2550 consumers at retail outlets in RWANDA: Discrepancies in ever use of condoms and risky sexual behaviours are due to differences in socioeconomic status of the two samples. After controls, exit surveys at most outlet types have the same results as the household survey. Only exit surveys at bars, nightclubs and hotels yield significantly different estimates. However, the above-average knowledge of Prudence Plus condoms in the exit interviews is not attributable to socioeconomic or demographic variables, most likely because respondents have seen the product at the outlets. Information about condom use and sexual behaviour obtained from exit surveys appears as accurate as that obtained through household surveys. Nevertheless, exit surveys must be used cautiously. Because exit surveys may include wealthier and better-educated respondents, they are not representative of the general population. The composition of exit survey samples should be validated through existing household surveys. Comparisons across survey types are generally unadvisable, unless they control for sample differences. When generalizing to the population at large is not needed (e.g. for studies aimed at identifying the characteristics and behaviour of users of particular products or services), exit surveys can provide an appropriate alternative to household surveys.

  7. Remodeling of ribosomal genes in somatic cells by Xenopus egg extract

    Energy Technology Data Exchange (ETDEWEB)

    Ostrup, Olga, E-mail: osvarcova@gmail.com [Institute of Basic Animal and Veterinary Sciences, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C (Denmark); Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo (Norway); Norwegian Center for Stem Cell Research, Oslo (Norway); Hyttel, Poul; Klaerke, Dan A. [Institute of Basic Animal and Veterinary Sciences, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C (Denmark); Collas, Philippe, E-mail: philc@medisin.uio.no [Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo (Norway); Norwegian Center for Stem Cell Research, Oslo (Norway)

    2011-09-02

    Highlights: {yields} Xenopus egg extract remodels nuclei and alter cell growth characteristics. {yields} Ribosomal genes are reprogrammed within 6 h after extract exposure. {yields} rDNA reprogramming involves promoter targeting of SNF2H remodeling complex. {yields} Xenopus egg extract does not initiate stress-related response in somatic cells. {yields} Aza-cytidine elicits a stress-induced response in reprogrammed cells. -- Abstract: Extracts from Xenopus eggs can reprogram gene expression in somatic nuclei, however little is known about the earliest processes associated with the switch in the transcriptional program. We show here that an early reprogramming event is the remodeling of ribosomal chromatin and gene expression. This occurs within hours of extract treatment and is distinct from a stress response. Egg extract elicits remodeling of the nuclear envelope, chromatin and nucleolus. Nucleolar remodeling involves a rapid and stable decrease in ribosomal gene transcription, and promoter targeting of the nucleolar remodeling complex component SNF2H without affecting occupancy of the transcription factor UBF and the stress silencers SUV39H1 and SIRT1. During this process, nucleolar localization of UBF and SIRT1 is not altered. On contrary, azacytidine pre-treatment has an adverse effect on rDNA remodeling induced by extract and elicits a stress-type nuclear response. Thus, an early event of Xenopus egg extract-mediated nuclear reprogramming is the remodeling of ribosomal genes involving nucleolar remodeling complex. Condition-specific and rapid silencing of ribosomal genes may serve as a sensitive marker for evaluation of various reprogramming methods.

  8. Diamond Blackfan Anemia at the Crossroad between Ribosome Biogenesis and Heme Metabolism

    Directory of Open Access Journals (Sweden)

    Deborah Chiabrando

    2010-01-01

    Full Text Available Diamond-Blackfan anemia (DBA is a rare, pure red-cell aplasia that presents during infancy. Approximately 40% of cases are associated with other congenital defects, particularly malformations of the upper limb or craniofacial region. Mutations in the gene coding for the ribosomal protein RPS19 have been identified in 25% of patients with DBA, with resulting impairment of 18S rRNA processing and 40S ribosomal subunit formation. Moreover, mutations in other ribosomal protein coding genes account for about 25% of other DBA cases. Recently, the analysis of mice from which the gene coding for the heme exporter Feline Leukemia Virus subgroup C Receptor (FLVCR1 is deleted suggested that this gene may be involved in the pathogenesis of DBA. FLVCR1-null mice show a phenotype resembling that of DBA patients, including erythroid failure and malformations. Interestingly, some DBA patients have disease linkage to chromosome 1q31, where FLVCR1 is mapped. Moreover, it has been reported that cells from DBA patients express alternatively spliced isoforms of FLVCR1 which encode non-functional proteins. Herein, we review the known roles of RPS19 and FLVCR1 in ribosome function and heme metabolism respectively, and discuss how the deficiency of a ribosomal protein or of a heme exporter may result in the same phenotype.

  9. Structural and functional organization of ribosomal genes within the mammalian cell nucleolus.

    Science.gov (United States)

    Derenzini, Massimo; Pasquinelli, Gianandrea; O'Donohue, Marie-Françoise; Ploton, Dominique; Thiry, Marc

    2006-02-01

    Data on the in situ structural-functional organization of ribosomal genes in the mammalian cell nucleolus are reviewed here. Major findings on chromatin structure in situ come from investigations carried out using the Feulgen-like osmium ammine reaction as a highly specific electron-opaque DNA tracer. Intranucleolar chromatin shows three different levels of organization: compact clumps, fibers ranging from 11 to 30 nm, and loose agglomerates of extended DNA filaments. Both clumps and fibers of chromatin exhibit a nucleosomal organization that is lacking in the loose agglomerates of extended DNA filaments. In fact, these filaments constantly show a thickness of 2-3 nm, the same as a DNA double-helix molecule. The loose agglomerates of DNA filaments are located in the fibrillar centers, the interphase counterpart of metaphase NORs, therefore being constituted by ribosomal DNA. The extended, non-nucleosomal configuration of this rDNA has been shown to be independent of transcriptional activity and characterizes ribosome genes that are either transcribed or transcriptionally silent. Data reviewed are consistent with a model of control for ribosome gene activity that is not mediated by changes in chromatin structure. The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.

  10. Development of the tunneling junction simulation environment for scanning tunneling microscope evaluation

    International Nuclear Information System (INIS)

    Gajewski, Krzysztof; Piasecki, Tomasz; Kopiec, Daniel; Gotszalk, Teodor

    2017-01-01

    Proper configuration of scanning tunneling microscope electronics plays an important role in the atomic scale resolution surface imaging. Device evaluation in the tunneling contact between scanning tip and sample may be prone to the surface quality or mechanical disturbances. Thus the use of tunneling junction simulator makes electronics testing more reliable and increases its repeatability. Here, we present the theoretical background enabling the proper selection of electronic components circuitry used as a tunneling junction simulator. We also show how to simulate mechanics related to the piezoelectric scanner, which is applied in real experiments. Practical use of the proposed simulator and its application in metrological characterization of the developed scanning tunneling microscope is also shown. (paper)

  11. Fabrication of magnetic tunnel junctions with a single-crystalline LiF tunnel barrier

    Science.gov (United States)

    Krishna Narayananellore, Sai; Doko, Naoki; Matsuo, Norihiro; Saito, Hidekazu; Yuasa, Shinji

    2018-04-01

    We fabricated Fe/LiF/Fe magnetic tunnel junctions (MTJs) by molecular beam epitaxy on a MgO(001) substrate, where LiF is an insulating tunnel barrier with the same crystal structure as MgO (rock-salt type). Crystallographical studies such as transmission electron microscopy and nanobeam electron diffraction observations revealed that the LiF tunnel barrier is single-crystalline and has a LiF(001)[100] ∥ bottom Fe(001)[110] crystal orientation, which is constructed in the same manner as MgO(001) on Fe(001). Also, the in-plane lattice mismatch between the LiF tunnel barrier and the Fe bottom electrode was estimated to be small (about 0.5%). Despite such advantages for the tunnel barrier of the MTJ, the observed tunnel magnetoresistance (MR) ratio was low (˜6% at 20 K) and showed a significant decrease with increasing temperature (˜1% at room temperature). The results imply that indirect tunneling and/or thermally excited carriers in the LiF tunnel barrier, in which the current basically is not spin-polarized, play a major role in electrical transport in the MTJ.

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

    DEFF Research Database (Denmark)

    Latif, Haythem; Szubin, Richard; Tan, Justin

    2015-01-01

    Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used...... in the microbial research community. Here we present a streamlined ribosome profiling protocol with reduced barriers to entry for microbial characterization studies. Our approach provides simplified alternatives during harvest, lysis, and recovery of monosomes and also eliminates several time-consuming steps...

  13. Ethnic variations in immigrant poverty exit and female employment: the missing link.

    Science.gov (United States)

    Kaida, Lisa

    2015-04-01

    Despite widespread interest in poverty among recent immigrants and female immigrant employment, research on the link between the two is limited. This study evaluates the effect of recently arrived immigrant women's employment on the exit from family poverty and considers the implications for ethnic differences in poverty exit. It uses the bivariate probit model and the Fairlie decomposition technique to analyze data from the Longitudinal Survey of Immigrants to Canada (LSIC), a nationally representative survey of immigrants arriving in Canada, 2000-2001. Results show that the employment of recently arrived immigrant women makes a notable contribution to lifting families out of poverty. Moreover, the wide ethnic variations in the probability of exit from poverty between European and non-European groups are partially explained by the lower employment rates among non-European women. The results suggest that the equal earner/female breadwinner model applies to low-income recent immigrant families in general, but the male breadwinner model explains the low probability of poverty exit among select non-European groups whose female employment rates are notably low.

  14. Is The Ribosome Targeted By Adaptive Mutations

    DEFF Research Database (Denmark)

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

    2015-01-01

    Introduction: RNA polymerase and ribosomes, composing the macromolecular synthesis machinery (MMSM), carry out the central processes of transcription and translation, but are usually seen as mechanical elements with no regulatory function. Extensive investigations of gene regulation and the high ...

  15. Mean-Variance portfolio optimization when each asset has individual uncertain exit-time

    Directory of Open Access Journals (Sweden)

    Reza Keykhaei

    2016-12-01

    Full Text Available The standard Markowitz Mean-Variance optimization model is a single-period portfolio selection approach where the exit-time (or the time-horizon is deterministic. ‎In this paper we study the Mean-Variance portfolio selection problem ‎with ‎uncertain ‎exit-time ‎when ‎each ‎has ‎individual uncertain ‎xit-time‎, ‎which generalizes the Markowitz's model‎. ‎‎‎‎‎‎We provide some conditions under which the optimal portfolio of the generalized problem is independent of the exit-times distributions. Also, ‎‎it is shown that under some general circumstances, the sets of optimal portfolios‎ ‎in the generalized model and the standard model are the same‎.

  16. Resonant tunneling via spin-polarized barrier states in a magnetic tunnel junction

    NARCIS (Netherlands)

    Jansen, R.; Lodder, J.C.

    2000-01-01

    Resonant tunneling through states in the barrier of a magnetic tunnel junction has been analyzed theoretically for the case of a spin-polarized density of barrier states. It is shown that for highly spin-polarized barrier states, the magnetoresistance due to resonant tunneling is enhanced compared

  17. Quantum tunneling time

    International Nuclear Information System (INIS)

    Wang, Z.S.; Lai, C.H.; Oh, C.H.; Kwek, L.C.

    2004-01-01

    We present a calculation of quantum tunneling time based on the transition duration of wave peak from one side of a barrier to the other. In our formulation, the tunneling time comprises a real and an imaginary part. The real part is an extension of the phase tunneling time with quantum corrections whereas the imaginary time is associated with energy derivatives of the probability amplitudes

  18. 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

  19. rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

    OpenAIRE

    O?Connor, Patrick B. F.; Li, Gene-Wei; Weissman, Jonathan S.; Atkins, John F.; Baranov, Pavel V.

    2013-01-01

    Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine?Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide...

  20. Acrolein preferentially damages nucleolus eliciting ribosomal stress and apoptosis in human cancer cells.

    Science.gov (United States)

    Wang, Hsiang-Tsui; Chen, Tzu-Ying; Weng, Ching-Wen; Yang, Chun-Hsiang; Tang, Moon-Shong

    2016-12-06

    Acrolein (Acr) is a potent cytotoxic and DNA damaging agent which is ubiquitous in the environment and abundant in tobacco smoke. Acr is also an active cytotoxic metabolite of the anti-cancer drugs cyclophosphamide and ifosfamide. The mechanisms via which Acr exerts its anti-cancer activity and cytotoxicity are not clear. In this study, we found that Acr induces cytotoxicity and cell death in human cancer cells with different activities of p53. Acr preferentially binds nucleolar ribosomal DNA (rDNA) to form Acr-deoxyguanosine adducts, and induces oxidative damage to both rDNA and ribosomal RNA (rRNA). Acr triggers ribosomal stress responses, inhibits rRNA synthesis, reduces RNA polymerase I binding to the promoter of rRNA gene, disrupts nucleolar integrity, and impairs ribosome biogenesis and polysome formation. Acr causes an increase in MDM2 levels and phosphorylation of MDM2 in A549 and HeLa cells which are p53 active and p53 inactive, respectively. It enhances the binding of ribosomal protein RPL11 to MDM2 and reduces the binding of p53 and E2F-1 to MDM2 resulting in stabilization/activation of p53 in A549 cells and degradation of E2F-1 in A549 and HeLa cells. We propose that Acr induces ribosomal stress which leads to activation of MDM2 and RPL11-MDM2 binding, consequently, activates p53 and enhances E2F-1 degradation, and that taken together these two processes induce apoptosis and cell death.

  1. Ecologies of ideologies : Explaining party entry and exit in European parliaments, 1945-2013

    NARCIS (Netherlands)

    van de Wardt, Marc; Berkhout, Joost; Vermeulen, Floris

    This study introduces a population-ecological approach to the entry and exit of political parties. A primary proposition of population ecology is that organizational entry and exit depends on the number of organizations already present: that is, density. We propose that political parties mainly

  2. Measuring fire size in tunnels

    International Nuclear Information System (INIS)

    Guo, Xiaoping; Zhang, Qihui

    2013-01-01

    A new measure of fire size Q′ has been introduced in longitudinally ventilated tunnel as the ratio of flame height to the height of tunnel. The analysis in this article has shown that Q′ controls both the critical velocity and the maximum ceiling temperature in the tunnel. Before the fire flame reaches tunnel ceiling (Q′ 1.0), Fr approaches a constant value. This is also a well-known phenomenon in large tunnel fires. Tunnel ceiling temperature shows the opposite trend. Before the fire flame reaches the ceiling, it increases very slowly with the fire size. Once the flame has hit the ceiling of tunnel, temperature rises rapidly with Q′. The good agreement between the current prediction and three different sets of experimental data has demonstrated that the theory has correctly modelled the relation among the heat release rate of fire, ventilation flow and the height of tunnel. From design point of view, the theoretical maximum of critical velocity for a given tunnel can help to prevent oversized ventilation system. -- Highlights: • Fire sizing is an important safety measure in tunnel design. • New measure of fire size a function of HRR of fire, tunnel height and ventilation. • The measure can identify large and small fires. • The characteristics of different fire are consistent with observation in real fires

  3. Market entry and exit by biotech and device companies funded by venture capital.

    Science.gov (United States)

    Burns, Lawton R; Housman, Michael G; Robinson, Charles A

    2009-01-01

    Start-up companies in the biotechnology and medical device sectors are important sources of health care innovation. This paper describes the role of venture capital in supporting these companies and charts the growth in venture capital financial support. The paper then uses longitudinal data to describe market entry and exit by these companies. Similar factors are associated with entry and exit in the two sectors. Entries and exits in one sector also appear to influence entry in the other. These findings have important implications for developing innovative technologies and ensuring competitive markets in the life sciences.

  4. Microwave-induced co-tunneling in single electron tunneling transistors

    DEFF Research Database (Denmark)

    Ejrnaes, M.; Savolainen, M.; Manscher, M.

    2002-01-01

    on rubber bellows. Cross-talk was minimized by using individual coaxial lines between the sample and the room temperature electronics: The co-tunneling experiments were performed at zero DC bias current by measuring the voltage response to a very small amplitude 2 Hz current modulation with the gate voltage......The influence of microwaves on the co-tunneling in single electron tunneling transistors has been investigated as function of frequency and power in the temperature range from 150 to 500 mK. All 20 low frequency connections and the RF line were filtered, and the whole cryostat was suspended...

  5. Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory.

    Science.gov (United States)

    Suarez, Stéphanie; Ferroni, Agnès; Lotz, Aurélie; Jolley, Keith A; Guérin, Philippe; Leto, Julie; Dauphin, Brunhilde; Jamet, Anne; Maiden, Martin C J; Nassif, Xavier; Armengaud, Jean

    2013-09-01

    Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of microorganisms that is increasingly used in microbiology laboratories. This identification is based on the comparison of the tested isolate mass spectrum with reference databases. Using Neisseria meningitidis as a model organism, we showed that in one of the available databases, the Andromas database, 10 of the 13 species-specific biomarkers correspond to ribosomal proteins. Remarkably, one biomarker, ribosomal protein L32, was subject to inter-strain variability. The analysis of the ribosomal protein patterns of 100 isolates for which whole genome sequences were available, confirmed the presence of inter-strain variability in the molecular weight of 29 ribosomal proteins, thus establishing a correlation between the sequence type (ST) and/or clonal complex (CC) of each strain and its ribosomal protein pattern. Since the molecular weight of three of the variable ribosomal proteins (L30, L31 and L32) was included in the spectral window observed by MALDI-TOF MS in clinical microbiology, i.e., 3640-12000 m/z, we were able by analyzing the molecular weight of these three ribosomal proteins to classify each strain in one of six subgroups, each of these subgroups corresponding to specific STs and/or CCs. Their detection by MALDI-TOF allows therefore a quick typing of N. meningitidis isolates. © 2013 Elsevier B.V. All rights reserved.

  6. Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana.

    Science.gov (United States)

    Palm, Denise; Simm, Stefan; Darm, Katrin; Weis, Benjamin L; Ruprecht, Maike; Schleiff, Enrico; Scharf, Christian

    2016-01-01

    Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for Saccharomyces cerevisiae. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of Arabidopsis thaliana and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.

  7. Influence of trap-assisted tunneling on trap-assisted tunneling current in double gate tunnel field-effect transistor

    International Nuclear Information System (INIS)

    Jiang Zhi; Zhuang Yi-Qi; Li Cong; Wang Ping; Liu Yu-Qi

    2016-01-01

    Trap-assisted tunneling (TAT) has attracted more and more attention, because it seriously affects the sub-threshold characteristic of tunnel field-effect transistor (TFET). In this paper, we assess subthreshold performance of double gate TFET (DG-TFET) through a band-to-band tunneling (BTBT) model, including phonon-assisted scattering and acoustic surface phonons scattering. Interface state density profile (D it ) and the trap level are included in the simulation to analyze their effects on TAT current and the mechanism of gate leakage current. (paper)

  8. Toxicity of ricin A chain is reduced in mammalian cells by inhibiting its interaction with the ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Jetzt, Amanda E. [Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520 (United States); Li, Xiao-Ping; Tumer, Nilgun E. [Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520 (United States); Cohick, Wendie S., E-mail: cohick@aesop.rutgers.edu [Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520 (United States)

    2016-11-01

    Ricin is a potent ribotoxin that is considered a bioterror threat due to its ease of isolation and possibility of aerosolization. In yeast, mutation of arginine residues away from the active site results in a ricin toxin A chain (RTA) variant that is unable to bind the ribosome and exhibits reduced cytotoxicity. The goal of the present work was to determine if these residues contribute to ribosome binding and cytotoxicity of RTA in mammalian cells. The RTA mutant R193A/R235A did not interact with mammalian ribosomes, while a G212E variant with a point mutation near its active site bound ribosomes similarly to wild-type (WT) RTA. R193A/R235A retained full catalytic activity on naked RNA but had reduced activity on mammalian ribosomes. To determine the effect of this mutant in intact cells, pre R193A/R235A containing a signal sequence directing it to the endoplasmic reticulum and mature R193A/R235A that directly targeted cytosolic ribosomes were each expressed. Depurination and protein synthesis inhibition were reduced by both pre- and mature R193A/R235A relative to WT. Protein synthesis inhibition was reduced to a greater extent by R193A/R235A than by G212E. Pre R193A/R235A caused a greater reduction in caspase activation and loss of mitochondrial membrane potential than G212E relative to WT RTA. These findings indicate that an RTA variant with reduced ribosome binding is less toxic than a variant with less catalytic activity but normal ribosome binding activity. The toxin-ribosome interaction represents a novel target for the development of therapeutics to prevent or treat ricin intoxication. - Highlights: • Arginines 193 and 235 of RTA are critical for binding to the mammalian ribosome. • R193A/R235A has full catalytic activity on RNA but not on mammalian ribosomes. • R193A/R235A is less toxic than a mutant that targets the active site. • The toxin-ribosome interaction is a therapeutic target for ricin intoxication.

  9. Generation of monoclonal antibodies for the assessment of protein purification by recombinant ribosomal coupling

    DEFF Research Database (Denmark)

    Kristensen, Janni; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk

    2005-01-01

    We recently described a conceptually novel method for the purification of recombinant proteins with a propensity to form inclusion bodies in the cytoplasm of Escherichia coli. Recombinant proteins were covalently coupled to the E. coli ribosome by fusing them to ribosomal protein 23 (rpL23...... therefore purified rpL23-GFP-His, rpL23-His and GFP from E. coli recombinants using affinity, ion exchange and hydrophobic interaction chromatography. These proteins could be purified with yields of 150, 150 and 1500 microg per gram cellular wet weight, respectively. However, rpL23-GFP-His could only...... proteolytic cleavage sites. We conclude that the generated antibodies can be used to evaluate ribosomal coupling of recombinant target proteins as well as the efficiency of their separation from the ribosome....

  10. Thermovoltages in vacuum tunneling investigated by scanning tunneling microscopy

    OpenAIRE

    Hoffmann, D. H.; Rettenberger, Armin; Grand, Jean Yves; Läuger, K.; Leiderer, Paul; Dransfeld, Klaus; Möller, Rolf

    1995-01-01

    By heating the tunneling tip of a scanning tunneling microscope the thermoelectric properties of a variable vacuum barrier have been investigated. The lateral variation of the observed thermovoltage will be discussed for polycrystalline gold, stepped surfaces of silver, as well as for copper islands on silver.

  11. Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii

    Institute of Scientific and Technical Information of China (English)

    Zhifei Li; Qiang Guo; Lvqin Zheng; Yongsheng Ji; Yi-Ting Xie; De-Hua Lai; Zhao-Rong Lun; Xun Suo; Ning Gao

    2017-01-01

    As an indispensable molecular machine universal in all living organisms,the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors.High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes.With cryo-electron microscopy technique,we have determined structures of the cytosolic ribosomes from two human parasites,Trichomonas vaginalis and Toxoplasma gondii,at resolution of 3.2-3.4,(A).Although the ribosomal proteins from both pathogens are typical members of eukaryotic families,with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments,the sizes of their rRNAs are sharply different.Very interestingly,rRNAs of T.vaginalis are in size comparable to prokaryotic counterparts,with nearly all the eukaryote-specific rRNA expansion segments missing.These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs,and may aid in design of novel translation inhibitors.

  12. Macroscopic quantum tunneling in Josephson tunnel junctions and Coulomb blockade in single small tunnel junctions

    International Nuclear Information System (INIS)

    Cleland, A.N.

    1991-04-01

    Experiments investigating the process of macroscopic quantum tunneling in a moderately-damped, resistively shunted, Josephson junction are described, followed by a discussion of experiments performed on very small capacitance normal-metal tunnel junctions. The experiments on the resistively-shunted Josephson junction were designed to investigate a quantum process, that of the tunneling of the Josephson phase variable under a potential barrier, in a system in which dissipation plays a major role in the dynamics of motion. All the parameters of the junction were measured using the classical phenomena of thermal activation and resonant activation. Theoretical predictions are compared with the experimental results, showing good agreement with no adjustable parameters; the tunneling rate in the moderately damped (Q ∼ 1) junction is seen to be reduced by a factor of 300 from that predicted for an undamped junction. The phase is seen to be a good quantum-mechanical variable. The experiments on small capacitance tunnel junctions extend the measurements on the larger-area Josephson junctions from the region in which the phase variable has a fairly well-defined value, i.e. its wavefunction has a narrow width, to the region where its value is almost completely unknown. The charge on the junction becomes well-defined and is predicted to quantize the current through the junction, giving rise to the Coulomb blockade at low bias. I present the first clear observation of the Coulomb blockade in single junctions. The electrical environment of the tunnel junction, however, strongly affects the behavior of the junction: higher resistance leads are observed to greatly sharpen the Coulomb blockade over that seen with lower resistance leads. I present theoretical descriptions of how the environment influences the junctions; comparisons with the experimental results are in reasonable agreement

  13. Wives' Relative Wages, Husbands' Paid Work Hours, and Wives' Labor-Force Exit

    Science.gov (United States)

    Shafer, Emily Fitzgibbons

    2011-01-01

    Economic theories predict that women are more likely to exit the labor force if their partners' earnings are higher and if their own wage rate is lower. In this article, I use the National Longitudinal Survey of Youth (N = 2,254) and discrete-time event-history analysis to show that wives' relative wages are more predictive of their exit than are…

  14. About tunnelling times

    International Nuclear Information System (INIS)

    Olkhovsky, V.S.; Recami, E.

    1991-08-01

    In this paper, first we critically analyse the main theoretical definitions and calculations of the sub-barrier tunnelling and reflection times. Secondly, we propose a new, physically sensible definition of such durations, on the basis of a recent general formalism (already tested for other types of quantum collisions). At last, we discuss some results regarding temporal evolution of the tunnelling processes, and in particular the ''particle'' speed during tunnelling. (author). 36 refs, 1 fig

  15. First exit times of harmonically trapped particles: a didactic review

    International Nuclear Information System (INIS)

    Grebenkov, Denis S

    2015-01-01

    We revise the classical problem of characterizing first exit times of a harmonically trapped particle whose motion is described by a one- or multidimensional Ornstein–Uhlenbeck process. We start by recalling the main derivation steps of a propagator using Langevin and Fokker–Planck equations. The mean exit time, the moment-generating function and the survival probability are then expressed through confluent hypergeometric functions and thoroughly analyzed. We also present a rapidly converging series representation of confluent hypergeometric functions that is particularly well suited for numerical computation of eigenvalues and eigenfunctions of the governing Fokker–Planck operator. We discuss several applications of first exit times, such as the detection of time intervals during which motor proteins exert a constant force onto a tracer in optical tweezers single-particle tracking experiments; adhesion bond dissociation under mechanical stress; characterization of active periods of trend-following and mean-reverting strategies in algorithmic trading on stock markets; relation to the distribution of first crossing times of a moving boundary by Brownian motion. Some extensions are described, including diffusion under quadratic double-well potential and anomalous diffusion. (topical review)

  16. Tunneling current between graphene layers

    OpenAIRE

    Poklonski, Nikolai A.; Siahlo, Andrei I.; Vyrko, Sergey A.; Popov, Andrey M.; Lozovik, Yurii E.

    2013-01-01

    The physical model that allows to calculate the values of the tunneling current be-tween graphene layers is proposed. The tunneling current according to the pro-posed model is proportional to the area of tunneling transition. The calculated value of tunneling conductivity is in qualitative agreement with experimental data.

  17. Evidence for alteration of the membrane-bound ribosomes in Micrococcus luteus cells exposed to lead

    Energy Technology Data Exchange (ETDEWEB)

    Barrow, W; Himmel, M; Squire, P G; Tornabene, T G

    1978-01-01

    Micrococcus luteus cells exposed to Pb(NO/sub 3/)/sub 2/ contained cytosol ribosomal particles and disaggregated membranal ribosomal particles as determined by ultracentrifugation and spectral studies. Approximately 60% of the membrane ribosome fraction from lead exposed cells had a sedimentation value of 8.4S. Cytosol ribosome from lead exposed cells as well as membranal and cytosol ribosomes from control cells were comparable by their contents of predominantly the 70S type with the 50S and 100S present in relatively small amounts. The lead content of the 8.4S components was more than 200 times higher than the components with higher sedimentation coefficients from lead exposed cells and approximately 650 times more than that of control cell ribosomes. The cells exposed to lead, however, showed no adverse effects from the lead in respect to their growth rates and cellular yields. These results indicate that lead is interacting only at specific sites of the membrane and is inducing events initiated only in strategic cellular regions. These data further substantiate that subtle changes do occur in lead exposed cells that show no obvious effects. It is assumed that these minor alterations are, in toto, biologically significant. 24 references, 2 figures, 1 table.

  18. Assembly constraints drive co-evolution among ribosomal constituents.

    Science.gov (United States)

    Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

    2015-06-23

    Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Interaction of pleuromutilin derivatives with the ribosomal peptidyl transferase center

    DEFF Research Database (Denmark)

    Long, K. S.; Hansen, L. K.; Jakobsen, L.

    2006-01-01

    Tiamulin is a pleuromutilin antibiotic that is used in veterinary medicine. The recently published crystal structure of a tiamulin-50S ribosomal subunit complex provides detailed information about how this drug targets the peptidyl transferase center of the ribosome. To promote rational design...... mutant strain is resistant to tiamulin and pleuromutilin, but not valnemulin, implying that valnemulin is better able to withstand an altered rRNA binding surface around the mutilin core. This is likely due to additional interactions made between the valnemulin side chain extension and the rRNA binding...

  20. Production of RNA-protein cross links in γ irradiated E. Coli ribosomes

    International Nuclear Information System (INIS)

    Ekert, Bernard; Giocanti, Nicole

    1976-01-01

    γ irradiation in de-aerated conditions of E. coli MRE 600 ribosomes, labelled with 14 C uracil, leads to a decrease of extractibility of 14 C RNA by lithium chloride 4 M-urea 8 M. On the other hand, the radioactivity of the protein fraction increases with irradiation. These results strongly suggest that RNA-protein cross links are formed in irradiated ribosomes [fr

  1. Analysis of the protein-protein interactions between the human acidic ribosomal P-proteins: evaluation by the two hybrid system

    DEFF Research Database (Denmark)

    Tchórzewski, M; Boldyreff, B; Issinger, O

    2000-01-01

    The surface acidic ribosomal proteins (P-proteins), together with ribosomal core protein P0 form a multimeric lateral protuberance on the 60 S ribosomal subunit. This structure, also called stalk, is important for efficient translational activity of the ribosome. In order to shed more light...... forms the 60 S ribosomal stalk: P0-(P1/P2)(2). Additionally, mutual interactions among human and yeast P-proteins were analyzed. Heterodimer formation could be observed between human P2 and yeast P1 proteins....

  2. Single Electron Tunneling

    International Nuclear Information System (INIS)

    Ruggiero, Steven T.

    2005-01-01

    Financial support for this project has led to advances in the science of single-electron phenomena. Our group reported the first observation of the so-called ''Coulomb Staircase'', which was produced by tunneling into ultra-small metal particles. This work showed well-defined tunneling voltage steps of width e/C and height e/RC, demonstrating tunneling quantized on the single-electron level. This work was published in a now well-cited Physical Review Letter. Single-electron physics is now a major sub-field of condensed-matter physics, and fundamental work in the area continues to be conducted by tunneling in ultra-small metal particles. In addition, there are now single-electron transistors that add a controlling gate to modulate the charge on ultra-small photolithographically defined capacitive elements. Single-electron transistors are now at the heart of at least one experimental quantum-computer element, and single-electron transistor pumps may soon be used to define fundamental quantities such as the farad (capacitance) and the ampere (current). Novel computer technology based on single-electron quantum dots is also being developed. In related work, our group played the leading role in the explanation of experimental results observed during the initial phases of tunneling experiments with the high-temperature superconductors. When so-called ''multiple-gap'' tunneling was reported, the phenomenon was correctly identified by our group as single-electron tunneling in small grains in the material. The main focus throughout this project has been to explore single electron phenomena both in traditional tunneling formats of the type metal/insulator/particles/insulator/metal and using scanning tunneling microscopy to probe few-particle systems. This has been done under varying conditions of temperature, applied magnetic field, and with different materials systems. These have included metals, semi-metals, and superconductors. Amongst a number of results, we have

  3. Drill and blast tunnelling; Konvensjonell drift av tunneler

    Energy Technology Data Exchange (ETDEWEB)

    Roenn, Paal-Egil

    1997-12-31

    This thesis treats drill and blast tunnelling. The rapid technological advance necessitates revised and updated design criteria, quality requirements and quality control. In situ blast experiments were carried out in order to test new methods and improve the basis for calculation and design. The main topics of the experiments were (1) longer rounds and increased drillhole diameter, (2) emulsion slurry as explosives in tunnelling, and (3) electronic detonators in contour blasting. The experiments show that it is technically feasible to blast rounds of up to 8.6 m length. Using current technology, the economical optimum round length is substantially shorter. Dust, low visibility, noise and toxic fumes are occupational environmental strains for the tunnel workers. Several of the environmental factors are strongly influenced by the type of explosives used. For example, emulsion slurry resulted in 4 to 5 times better visibility than Anolit and the concentration of respirable dust and total dust was reduced by 30-50 %. Electronic detonators were tested and found to give a higher percentage of remaining drillholes in the contour than Nonel detonators. The thesis includes a chapter on economic design of hydropower tunnels. 42 refs., 83 figs., 45 tabs.

  4. Resonant tunnel magnetoresistance in double-barrier planar magnetic tunnel junctions

    KAUST Repository

    Useinov, A. N.

    2011-08-24

    We present a theoretical approach to calculate the spin-dependent current and tunnel magnetoresistance (TMR) in a double-barrier magnetic tunnel junction (DMTJ), in which the magnetization of the middle ferromagnetic metal layer can be aligned parallel or antiparallel in relation to the fixed magnetizations of the left and right ferromagnetic electrodes. The electron transport through the DMTJ is considered as a three-dimensional problem, taking into account all transmitting electron trajectories as well as the spin-dependent momentum conservation law. The dependence of the transmission coefficient and spin-polarized currents on the applied voltage is derived as an exact solution to the quantum-mechanical problem for the spin-polarized transport. In the range of the developed physical model, the resonant tunneling, nonresonant tunneling, and enhanced spin filtering can be explained; the simulation results are in good agreement with experimental data.

  5. Resonant tunnel magnetoresistance in double-barrier planar magnetic tunnel junctions

    KAUST Repository

    Useinov, A. N.; Kosel, Jü rgen; Useinov, N. Kh.; Tagirov, L. R.

    2011-01-01

    We present a theoretical approach to calculate the spin-dependent current and tunnel magnetoresistance (TMR) in a double-barrier magnetic tunnel junction (DMTJ), in which the magnetization of the middle ferromagnetic metal layer can be aligned parallel or antiparallel in relation to the fixed magnetizations of the left and right ferromagnetic electrodes. The electron transport through the DMTJ is considered as a three-dimensional problem, taking into account all transmitting electron trajectories as well as the spin-dependent momentum conservation law. The dependence of the transmission coefficient and spin-polarized currents on the applied voltage is derived as an exact solution to the quantum-mechanical problem for the spin-polarized transport. In the range of the developed physical model, the resonant tunneling, nonresonant tunneling, and enhanced spin filtering can be explained; the simulation results are in good agreement with experimental data.

  6. Inhibition of the mitotic exit network in response to damaged telomeres.

    Directory of Open Access Journals (Sweden)

    Mauricio Valerio-Santiago

    Full Text Available When chromosomal DNA is damaged, progression through the cell cycle is halted to provide the cells with time to repair the genetic material before it is distributed between the mother and daughter cells. In Saccharomyces cerevisiae, this cell cycle arrest occurs at the G2/M transition. However, it is also necessary to restrain exit from mitosis by maintaining Bfa1-Bub2, the inhibitor of the Mitotic Exit Network (MEN, in an active state. While the role of Bfa1 and Bub2 in the inhibition of mitotic exit when the spindle is not properly aligned and the spindle position checkpoint is activated has been extensively studied, the mechanism by which these proteins prevent MEN function after DNA damage is still unclear. Here, we propose that the inhibition of the MEN is specifically required when telomeres are damaged but it is not necessary to face all types of chromosomal DNA damage, which is in agreement with previous data in mammals suggesting the existence of a putative telomere-specific DNA damage response that inhibits mitotic exit. Furthermore, we demonstrate that the mechanism of MEN inhibition when telomeres are damaged relies on the Rad53-dependent inhibition of Bfa1 phosphorylation by the Polo-like kinase Cdc5, establishing a new key role of this kinase in regulating cell cycle progression.

  7. Ribosomal binding region for the antibiotic tiamulin: stoichiometry, subunit location, and affinity for various analogs.

    Science.gov (United States)

    Högenauer, G; Ruf, C

    1981-01-01

    Equilibrium dialysis experiments with a highly purified preparation of labeled tiamulin, a semisynthetic derivative of the antibiotic pleuromutilin, and Escherichia coli ribosomes allowed the determination of two binding sites for the drug. The binding reaction showed a cooperative effect. Of the two subunits, the 50S particle was able to bind the antibiotic in a 1:1 stoichiometry. Hence, the 50S subunit contributed predominantly to the binding energy which held the antibiotic to the ribosomes. The 30S subunit, showing no strong affinity for the drug, may be needed for the generation of the second binding site in the 70S particle. If depleted of ammonium ions, 70S ribosomes lost their binding capacity for the antibiotic. The attachment sites for tiamulin could be restored by heating the ribosomes to 40 degrees C in the presence of either ammonium ions or the antibiotic. Other pleuromutilin derivatives displaced labeled tiamulin from its ribosomal binding sites. By quantifying this competition, the relative affinity of various pleuromutilin derivatives for E. coli ribosomes was determined. The binding correlated with the minimal inhibitory concentrations of these compounds against E. coli. When compared with the minimal inhibitory concentrations of these compounds against E. coli. When compared with the minimal inhibitory concentrations against E. coli. When compared with the minimal inhibitory concentrations against Staphylococcus aureus, the correlation was less strict, but the same trend prevailed. These results suggest that the antibacterial activities of various pleuromutilin derivatives on a given test organism are mainly determined by the strength of binding to the ribosomes within the bacterial cell. PMID:6751216

  8. Visual Barriers to Prevent Ambulatory ALzheimer's Patients from Exiting through an Emergency Door.

    Science.gov (United States)

    Namazi, Kevan H.; And Others

    1989-01-01

    Conducted study on Alzheimer's unit to test seven different visual barrier conditions for reducing patient exits. Findings indicated that exiting was eliminated under two conditions. Results suggest visual agnosia, the inability to interpret what the eye sees, may be used as tool in managing wandering behavior of Alzheimer's patients. (Author/NB)

  9. Entrance, exit, and reentrance of one shot with a shotgun

    DEFF Research Database (Denmark)

    Gulmann, C; Hougen, H P

    1999-01-01

    The case being reported is one of a homicidal shotgun fatality with an unusual wound pattern. A 34-year-old man was shot at close range with a 12-gauge shotgun armed with No. 5 birdshot ammunition. The shot entered the left axillary region, exited through the left infraclavicular region, and ther......The case being reported is one of a homicidal shotgun fatality with an unusual wound pattern. A 34-year-old man was shot at close range with a 12-gauge shotgun armed with No. 5 birdshot ammunition. The shot entered the left axillary region, exited through the left infraclavicular region...

  10. Quantum size effects on spin-tunneling time in a magnetic resonant tunneling diode

    OpenAIRE

    Saffarzadeh, Alireza; Daqiq, Reza

    2009-01-01

    We study theoretically the quantum size effects of a magnetic resonant tunneling diode (RTD) with a (Zn,Mn)Se dilute magnetic semiconductor layer on the spin-tunneling time and the spin polarization of the electrons. The results show that the spin-tunneling times may oscillate and a great difference between the tunneling time of the electrons with opposite spin directions can be obtained depending on the system parameters. We also study the effect of structural asymmetry which is related to t...

  11. Formation Mechanisms for Entry and Exit Defects in Bobbin Friction Stir Welding

    Directory of Open Access Journals (Sweden)

    Abbas Tamadon

    2018-01-01

    Full Text Available Bobbin friction stir welding (BFSW is an innovative variant for the solid state welding process whereby a rotating symmetrical tool causes a fully penetrated bond. Despite the process development, there are still unknown variables in the characterization of the process parameters which can cause uncontrolled weld defects. The entry zone and the exit zone consist of two discontinuity-defects and removing them is one of the current challenges for improving the weld quality. In the present research, the characteristic features of the entry and exit defects in the weld structure and formation mechanism of them during the BFSW processing was investigated. Using stacked layers of multi-colour plasticine the material flow, analogous to metal flow, can be visualised. By using different colours as the path markers of the analogue model, the streamline flow can be easily delineated in the discontinuity defects compared with the metal welds. AA6082-T6 aluminium plates and multi-layered plasticine slabs were employed to replicate the entry-exit defects in the metal weld and analogue samples. The fixed-bobbin tool utilized for this research was optimized by adding a thread feature and tri-flat geometry to the pin and closed-end spiral scrolls on both shoulder surfaces. Samples were processed at different rotating and longitudinal speeds to show the degree of dependency on the welding parameters for the defects. The analogue models showed that the entry zone and the exit zone of the BFSW are affected by the inhomogeneity of the material flow regime which causes the ejection or disruption of the plastic flow in the gap between the bobbin shoulders. The trial aluminium welds showed that the elimination of entry-exit defects in the weld body is not completely possible but the size of the defects can be minimized by modification of the welding parameters. For the entry zone, the flow pattern evolution suggested formation mechanisms for a sprayed tail, island zone

  12. The impact of ill health on exit from paid employment in Europe among older workers.

    Science.gov (United States)

    van den Berg, Tilja; Schuring, Merel; Avendano, Mauricio; Mackenbach, Johan; Burdorf, Alex

    2010-12-01

    To determine the impact of ill health on exit from paid employment in Europe among older workers. Participants of the Survey on Health and Ageing in Europe (SHARE) in 11 European countries in 2004 and 2006 were selected when 50-63 years old and in paid employment at baseline (n=4611). Data were collected on self-rated health, chronic diseases, mobility limitations, obesity, smoking, alcohol use, physical activity and work characteristics. Participants were classified into employed, retired, unemployed and disabled at the end of the 2-year follow-up. Multinomial logistic regression was used to estimate the effect of different measures of ill health on exit from paid employment. During the 2-year follow-up, 17% of employed workers left paid employment, mainly because of early retirement. Controlling for individual and work related characteristics, poor self-perceived health was strongly associated with exit from paid employment due to retirement, unemployment or disability (ORs from 1.32 to 4.24). Adjustment for working conditions and lifestyle reduced the significant associations between ill health and exit from paid employment by 0-18.7%. Low education, obesity, low job control and effort-reward imbalance were associated with measures of ill health, but also risk factors for exit from paid employment after adjustment for ill health. Poor self-perceived health was strongly associated with exit from paid employment among European workers aged 50-63 years. This study suggests that the influence of ill health on exit from paid employment could be lessened by measures targeting obesity, problematic alcohol use, job control and effort-reward balance.

  13. Binding of Signal Recognition Particle Gives Ribosome/Nascent Chain Complexes a Competitive Advantage in Endoplasmic Reticulum Membrane Interaction

    Science.gov (United States)

    Neuhof, Andrea; Rolls, Melissa M.; Jungnickel, Berit; Kalies, Kai-Uwe; Rapoport, Tom A.

    1998-01-01

    Most secretory and membrane proteins are sorted by signal sequences to the endoplasmic reticulum (ER) membrane early during their synthesis. Targeting of the ribosome-nascent chain complex (RNC) involves the binding of the signal sequence to the signal recognition particle (SRP), followed by an interaction of ribosome-bound SRP with the SRP receptor. However, ribosomes can also independently bind to the ER translocation channel formed by the Sec61p complex. To explain the specificity of membrane targeting, it has therefore been proposed that nascent polypeptide-associated complex functions as a cytosolic inhibitor of signal sequence- and SRP-independent ribosome binding to the ER membrane. We report here that SRP-independent binding of RNCs to the ER membrane can occur in the presence of all cytosolic factors, including nascent polypeptide-associated complex. Nontranslating ribosomes competitively inhibit SRP-independent membrane binding of RNCs but have no effect when SRP is bound to the RNCs. The protective effect of SRP against ribosome competition depends on a functional signal sequence in the nascent chain and is also observed with reconstituted proteoliposomes containing only the Sec61p complex and the SRP receptor. We conclude that cytosolic factors do not prevent the membrane binding of ribosomes. Instead, specific ribosome targeting to the Sec61p complex is provided by the binding of SRP to RNCs, followed by an interaction with the SRP receptor, which gives RNC–SRP complexes a selective advantage in membrane targeting over nontranslating ribosomes. PMID:9436994

  14. The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading[OPEN

    Science.gov (United States)

    Missra, Anamika; Ernest, Ben; Jia, Qidong; Ke, Kenneth

    2015-01-01

    Circadian control of gene expression is well characterized at the transcriptional level, but little is known about diel or circadian control of translation. Genome-wide translation state profiling of mRNAs in Arabidopsis thaliana seedlings grown in long day was performed to estimate ribosome loading per mRNA. The experiments revealed extensive translational regulation of key biological processes. Notably, translation of mRNAs for ribosomal proteins and mitochondrial respiration peaked at night. Central clock mRNAs are among those subject to fluctuations in ribosome loading. There was no consistent phase relationship between peak translation states and peak transcript levels. The overlay of distinct transcriptional and translational cycles can be expected to alter the waveform of the protein synthesis rate. Plants that constitutively overexpress the clock gene CCA1 showed phase shifts in peak translation, with a 6-h delay from midnight to dawn or from noon to evening being particularly common. Moreover, cycles of ribosome loading that were detected under continuous light in the wild type collapsed in the CCA1 overexpressor. Finally, at the transcript level, the CCA1-ox strain adopted a global pattern of transcript abundance that was broadly correlated with the light-dark environment. Altogether, these data demonstrate that gene-specific diel cycles of ribosome loading are controlled in part by the circadian clock. PMID:26392078

  15. Two-Dimensional Bifurcated Inlet Variable Cowl Lip Test Completed in 10- by 10-Foot Supersonic Wind Tunnel

    Science.gov (United States)

    Hoffman, T. R.

    2000-01-01

    Researchers at the NASA Glenn Research Center at Lewis Field successfully tested a variable cowl lip inlet at simulated takeoff conditions in Glenn s 10- by 10-Foot Supersonic Wind Tunnel (10x10 SWT) as part of the High-Speed Research Program. The test was a follow-on to the Two-Dimensional Bifurcated (2DB) Inlet/Engine test. At the takeoff condition for a High-Speed Civil Transport aircraft, the inlet must provide adequate airflow to the engine with an acceptable distortion level and high-pressure recovery. The test was conducted to study the effectiveness of installing two rotating lips on the 2DB Inlet cowls to increase mass flow rate and eliminate or reduce boundary layer flow separation near the lips. Hardware was mounted vertically in the test section so that it extended through the tunnel ceiling and that the 2DB Inlet was exposed to the atmosphere above the test section. The tunnel was configured in the aerodynamic mode, and exhausters were used to pump down the tunnel to vacuum levels and to provide a maximum flow rate of approximately 58 lb/sec. The test determined the (1) maximum flow in the 2DB Inlet for each variable cowl lip, (2) distortion level and pressure recovery for each lip configuration, (3) boundary layer conditions near variable lips inside the 2DB Inlet, (4) effects of a wing structure adjacent to the 2DB Inlet, and (5) effects of different 2DB Inlet exit configurations. It also employed flow visualization to generate enough qualitative data on variable lips to optimize the variable lip concept. This test was a collaborative effort between the Boeing Company and Glenn. Extensive inhouse support at Glenn contributed significantly to the progress and accomplishment of this test.

  16. Influence of trap-assisted tunneling on trap-assisted tunneling current in double gate tunnel field-effect transistor

    Science.gov (United States)

    Zhi, Jiang; Yi-Qi, Zhuang; Cong, Li; Ping, Wang; Yu-Qi, Liu

    2016-02-01

    Trap-assisted tunneling (TAT) has attracted more and more attention, because it seriously affects the sub-threshold characteristic of tunnel field-effect transistor (TFET). In this paper, we assess subthreshold performance of double gate TFET (DG-TFET) through a band-to-band tunneling (BTBT) model, including phonon-assisted scattering and acoustic surface phonons scattering. Interface state density profile (Dit) and the trap level are included in the simulation to analyze their effects on TAT current and the mechanism of gate leakage current. Project supported by the National Natural Science Foundation of China (Grant Nos. 61574109 and 61204092).

  17. 49 CFR 238.113 - Emergency window exits.

    Science.gov (United States)

    2010-10-01

    ..., electrical locker, or kitchen); and (B) There are no more than eight seats in the seating area. (4) Cars with...), a bathroom, kitchen, or locomotive cab is not considered a “compartment.” (b) Ease of operability. On or after November 8, 1999, each emergency window exit shall be designed to permit rapid and easy...

  18. Study of tunneling transport in Si-based tunnel field-effect transistors with ON current enhancement utilizing isoelectronic trap

    Science.gov (United States)

    Mori, Takahiro; Morita, Yukinori; Miyata, Noriyuki; Migita, Shinji; Fukuda, Koichi; Mizubayashi, Wataru; Masahara, Meishoku; Yasuda, Tetsuji; Ota, Hiroyuki

    2015-02-01

    The temperature dependence of the tunneling transport characteristics of Si diodes with an isoelectronic impurity has been investigated in order to clarify the mechanism of the ON-current enhancement in Si-based tunnel field-effect transistors (TFETs) utilizing an isoelectronic trap (IET). The Al-N complex impurity was utilized for IET formation. We observed three types of tunneling current components in the diodes: indirect band-to-band tunneling (BTBT), trap-assisted tunneling (TAT), and thermally inactive tunneling. The indirect BTBT and TAT current components can be distinguished with the plot described in this paper. The thermally inactive tunneling current probably originated from tunneling consisting of two paths: tunneling between the valence band and the IET trap and tunneling between the IET trap and the conduction band. The probability of thermally inactive tunneling with the Al-N IET state is higher than the others. Utilization of the thermally inactive tunneling current has a significant effect in enhancing the driving current of Si-based TFETs.

  19. Photoaffinity labeling of the pactamycin binding site on eubacterial ribosomes

    International Nuclear Information System (INIS)

    Tejedor, F.; Amils, R.; Ballesta, J.P.

    1985-01-01

    Pactamycin, an inhibitor of the initial steps of protein synthesis, has an acetophenone group in its chemical structure that makes the drug a potentially photoreactive molecule. In addition, the presence of a phenolic residue makes it easily susceptible to radioactive labeling. Through iodination, one radioactive derivative of pactamycin has been obtained with biological activities similar to the unmodified drug when tested on in vivo and cell-free systems. With the use of [ 125 I]iodopactamycin, ribosomes of Escherichia coli have been photolabeled under conditions that preserve the activity of the particles and guarantee the specificity of the binding sites. Under these conditions, RNA is preferentially labeled when free, small ribosomal subunits are photolabeled, but proteins are the main target in the whole ribosome. This indicates that an important conformational change takes place in the binding site on association of the two subunits. The major labeled proteins are S2, S4, S18, S21, and L13. These proteins in the pactamycin binding site are probably related to the initiation step of protein synthesis

  20. Electrical installations of the Channel tunnel; Installations electriques du Tunnel sous la Manche

    Energy Technology Data Exchange (ETDEWEB)

    Kersabiec, G. de [Eurotunnel, Folkestone (United Kingdom)

    2002-08-01

    Like an underground factory, the railway and auxiliary equipments of the Channel tunnel between France and UK, need a reliable and redundant power supply with a high quality maintenance. This article presents: the design criteria of the power distribution systems, the installation itself and the organisation of its exploitation: 1 - transportation system of the Channel tunnel (loads to supply, exploitation imperatives, fundamental criteria); 2 - external power sources (connection to the UK and French grids, values used by the national grids); 3 - exploitation criteria, tunnel design; 4 - description (main UK and French power stations, 25 kV traction network, 21 kV distribution network, tunnels, lighting in railway tunnels, supply of terminals, earthing network); 5 - exploitation; 6 - maintenance and quality. (J.S.)

  1. Heavy-Atom Tunneling Calculations in Thirteen Organic Reactions: Tunneling Contributions are Substantial, and Bell's Formula Closely Approximates Multidimensional Tunneling at ≥250 K.

    Science.gov (United States)

    Doubleday, Charles; Armas, Randy; Walker, Dana; Cosgriff, Christopher V; Greer, Edyta M

    2017-10-09

    Multidimensional tunneling calculations are carried out for 13 reactions, to test the scope of heavy-atom tunneling in organic chemistry, and to check the accuracy of one-dimensional tunneling models. The reactions include pericyclic, cycloaromatization, radical cyclization and ring opening, and S N 2. When compared at the temperatures that give the same effective rate constant of 3×10 -5  s -1 , tunneling accounts for 25-95 % of the rate in 8 of the 13 reactions. Values of transmission coefficients predicted by Bell's formula, κ Bell  , agree well with multidimensional tunneling (canonical variational transition state theory with small curvature tunneling), κ SCT . Mean unsigned deviations of κ Bell vs. κ SCT are 0.08, 0.04, 0.02 at 250, 300 and 400 K. This suggests that κ Bell is a useful first choice for predicting transmission coefficients in heavy-atom tunnelling. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Synthesis and methylation of ribosomal RNA in HeLa cells infected with the herpes virus pseudorabies virus

    International Nuclear Information System (INIS)

    Furlong, J.C.; Kyriakidis, S.; Stevely, W.S.

    1982-01-01

    The effects of infection with the herpes virus pseudorabies virus on the metabolism of HeLa cell ribosomal RNA were examined. There is a decline both in the synthesis of nucleolar 45S ribosomal precursor RNA and in its processing to mature cytoplasmic RNA. The methylated oligonucleotides in the ribosomal RNA species were studied. The methylation of cytoplasmic ribosomal RNA was essentially unchanged. However there was some undermethylation of the nucleolar precursor. If undermethylated RNA does not mature then this may partly explain the reduced processing in the infected cells. (Author)

  3. Macroscopic quantum tunneling in Josephson tunnel junctions and Coulomb blockade in single small tunnel junctions

    International Nuclear Information System (INIS)

    Cleland, A.N.

    1991-01-01

    Experiments investigated the process of macroscopic quantum tunneling in a moderately-damped, resistively shunted, Josephson junction are described, followed by a discussion of experiments performed on very-small-capacitance normal-metal tunnel junctions. The experiments on the resistively-shunted Josephson junction were designed to investigate a quantum process, that of the tunneling of the Josephson-phase variable under a potential barrier, in a system in which dissipation plays a major role in the dynamics of motion. All the parameters of the junction were measured using the classical phenomena of thermal activation and resonant activation. Theoretical predictions are compared with the experimental results, showing good agreement with no adjustable parameters. The experiments on small-capacitance tunnel junctions extend the measurements on the large-area Josephson junctions from the region in which the phase variable has a fairly well-defined value, i.e. its wave function has a narrow width, to the region where its value is almost completely unknown. The charge on the junction becomes well-defined and is predicted to quantize the current through the junction, giving rise to the Coulomb blockade at low bias

  4. Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope.

    Science.gov (United States)

    Nazin, G V; Wu, S W; Ho, W

    2005-06-21

    The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends.

  5. Ribosomal and hematopoietic defects in induced pluripotent stem cells derived from Diamond Blackfan anemia patients.

    Science.gov (United States)

    Garçon, Loïc; Ge, Jingping; Manjunath, Shwetha H; Mills, Jason A; Apicella, Marisa; Parikh, Shefali; Sullivan, Lisa M; Podsakoff, Gregory M; Gadue, Paul; French, Deborah L; Mason, Philip J; Bessler, Monica; Weiss, Mitchell J

    2013-08-08

    Diamond Blackfan anemia (DBA) is a congenital disorder with erythroid (Ery) hypoplasia and tissue morphogenic abnormalities. Most DBA cases are caused by heterozygous null mutations in genes encoding ribosomal proteins. Understanding how haploinsufficiency of these ubiquitous proteins causes DBA is hampered by limited availability of tissues from affected patients. We generated induced pluripotent stem cells (iPSCs) from fibroblasts of DBA patients carrying mutations in RPS19 and RPL5. Compared with controls, DBA fibroblasts formed iPSCs inefficiently, although we obtained 1 stable clone from each fibroblast line. RPS19-mutated iPSCs exhibited defects in 40S (small) ribosomal subunit assembly and production of 18S ribosomal RNA (rRNA). Upon induced differentiation, the mutant clone exhibited globally impaired hematopoiesis, with the Ery lineage affected most profoundly. RPL5-mutated iPSCs exhibited defective 60S (large) ribosomal subunit assembly, accumulation of 12S pre-rRNA, and impaired erythropoiesis. In both mutant iPSC lines, genetic correction of ribosomal protein deficiency via complementary DNA transfer into the "safe harbor" AAVS1 locus alleviated abnormalities in ribosome biogenesis and hematopoiesis. Our studies show that pathological features of DBA are recapitulated by iPSCs, provide a renewable source of cells to model various tissue defects, and demonstrate proof of principle for genetic correction strategies in patient stem cells.

  6. NAD+ Is a Food Component That Promotes Exit from Dauer Diapause in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Mykola Mylenko

    Full Text Available The free-living soil nematode Caenorhabditis elegans adapts its development to the availability of food. When food is scarce and population density is high, worms enter a developmentally arrested non-feeding diapause stage specialized for long-term survival called the dauer larva. When food becomes available, they exit from the dauer stage, resume growth and reproduction. It has been postulated that compound(s present in food, referred to as the "food signal", promote exit from the dauer stage. In this study, we have identified NAD+ as a component of bacterial extract that promotes dauer exit. NAD+, when dissolved in alkaline medium, causes opening of the mouth and ingestion of food. We also show that to initiate exit from the dauer stage in response to NAD+ worms require production of serotonin. Thus, C. elegans can use redox cofactors produced by dietary organisms to sense food.

  7. Exit, voice, and loyalty in the Italian public health service: macroeconomic and corporate implications.

    Science.gov (United States)

    Ippolito, Adelaide; Impagliazzo, Cira; Zoccoli, Paola

    2013-01-01

    The paper analyses how customers of public health organizations can express their dissatisfaction for the services offered to them. The main aim is to evaluate the effects that possible dissatisfaction of Italian public health service customers can have on public health organizations. We adopted the methodological scheme developed by Hirschman with exit, voice, and loyalty, considering the macroeconomic and corporate implications that it causes for Italian public health organizations. The study investigated the effects developed by exit of the patients on the system of financing of local health authorities considering both the corporate level of analysis and the macroeconomic level. As a result, local health authority management is encouraged to pay greater attention to the exit phenomena through the adoption of tools that promote loyalty, such as the promotion of voice, even if exit is not promoting, at a macroeconomic level, considerable attention to this phenomenon.

  8. Exit, Voice, and Loyalty in the Italian Public Health Service: Macroeconomic and Corporate Implications

    Science.gov (United States)

    Impagliazzo, Cira; Zoccoli, Paola

    2013-01-01

    The paper analyses how customers of public health organizations can express their dissatisfaction for the services offered to them. The main aim is to evaluate the effects that possible dissatisfaction of Italian public health service customers can have on public health organizations. We adopted the methodological scheme developed by Hirschman with exit, voice, and loyalty, considering the macroeconomic and corporate implications that it causes for Italian public health organizations. The study investigated the effects developed by exit of the patients on the system of financing of local health authorities considering both the corporate level of analysis and the macroeconomic level. As a result, local health authority management is encouraged to pay greater attention to the exit phenomena through the adoption of tools that promote loyalty, such as the promotion of voice, even if exit is not promoting, at a macroeconomic level, considerable attention to this phenomenon. PMID:24348148

  9. Vacuum phonon tunneling.

    Science.gov (United States)

    Altfeder, Igor; Voevodin, Andrey A; Roy, Ajit K

    2010-10-15

    Field-induced phonon tunneling, a previously unknown mechanism of interfacial thermal transport, has been revealed by ultrahigh vacuum inelastic scanning tunneling microscopy (STM). Using thermally broadened Fermi-Dirac distribution in the STM tip as in situ atomic-scale thermometer we found that thermal vibrations of the last tip atom are effectively transmitted to sample surface despite few angstroms wide vacuum gap. We show that phonon tunneling is driven by interfacial electric field and thermally vibrating image charges, and its rate is enhanced by surface electron-phonon interaction.

  10. Breaking through the tranfer tunnel

    CERN Document Server

    Laurent Guiraud

    2001-01-01

    This image shows the tunnel boring machine breaking through the transfer tunnel into the LHC tunnel. Proton beams will be transferred from the SPS pre-accelerator to the LHC at 450 GeV through two specially constructed transfer tunnels. From left to right: LHC Project Director, Lyn Evans; CERN Director-General (at the time), Luciano Maiani, and Director for Accelerators, Kurt Hubner.

  11. New Tunneling Features in Polar III-Nitride Resonant Tunneling Diodes

    Directory of Open Access Journals (Sweden)

    Jimy Encomendero

    2017-10-01

    Full Text Available For the past two decades, repeatable resonant tunneling transport of electrons in III-nitride double barrier heterostructures has remained elusive at room temperature. In this work we theoretically and experimentally study III-nitride double-barrier resonant tunneling diodes (RTDs, the quantum transport characteristics of which exhibit new features that are unexplainable using existing semiconductor theory. The repeatable and robust resonant transport in our devices enables us to track the origin of these features to the broken inversion symmetry in the uniaxial crystal structure, which generates built-in spontaneous and piezoelectric polarization fields. Resonant tunneling transport enabled by the ground state as well as by the first excited state is demonstrated for the first time over a wide temperature window in planar III-nitride RTDs. An analytical transport model for polar resonant tunneling heterostructures is introduced for the first time, showing a good quantitative agreement with experimental data. From this model we realize that tunneling transport is an extremely sensitive measure of the built-in polarization fields. Since such electric fields play a crucial role in the design of electronic and photonic devices, but are difficult to measure, our work provides a completely new method to accurately determine their magnitude for the entire class of polar heterostructures.

  12. The architecture of mammalian ribosomal protein promoters

    Directory of Open Access Journals (Sweden)

    Perry Robert P

    2005-02-01

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

  13. Theoretical consideration of spin-polarized resonant tunneling in magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Mu Haifeng; Zhu Zhengang; Zheng Qingrong; Jin Biao; Wang Zhengchuan; Su Gang

    2004-01-01

    A recent elegant experimental realization [S. Yuasa et al., Science 297 (2002) 234] of the spin-polarized resonant tunneling in magnetic tunnel junctions is interpreted in terms of a two-band model. It is shown that the tunnel magnetoresistance (TMR) decays oscillatorily with the thickness of the normal metal (NM) layer, being fairly in agreement with the experimental observation. The tunnel conductance is found to decay with slight oscillations with the increase of the NM layer thickness, which is also well consistent with the experiment. In addition, when the magnetizations of both ferromagnet electrodes are not collinearly aligned, TMR is found to exhibit sharp resonant peaks at some particular thickness of the NM layer. The peaked TMR obeys nicely a Gaussian distribution against the relative orientation of the magnetizations

  14. Histological Observation of Regions around Bone Tunnels after Compression of the Bone Tunnel Wall in Ligament Reconstruction

    International Nuclear Information System (INIS)

    Maeda, Shintaro; Ishikawa, Hiroki; Tanigawa, Naoaki; Miyazaki, Kyosuke; Shioda, Seiji

    2012-01-01

    The objectives of this study were to investigate the time-course of influence of compression of bone tunnel wall in ligament reconstruction on tissue around the bone tunnel and to histologically examine the mechanism of preventing the complication of bone tunnel dilation, using rabbit tibia. A model in which the femoral origin of the extensor digitorum longus tendon was cut and inserted into a bone tunnel made proximal to the tibia was prepared in the bilateral hind legs of 20 Japanese white rabbits. In each animal, a tunnel was made using a drill only in the right leg, while an undersized bone tunnel was made by drilling and then dilated by compression using a dilator to the same tunnel size as that in the right leg. Animals were sacrificed at 0, 2, 4, 8 and 12 weeks after surgery (4 animals at each time point). Observation of bone tunnels by X-ray radiography showed osteosclerosis in the 2- and 4-week dilation groups. Osteosclerosis appeared as white lines around the bone tunnel on X-ray radiography. This suggests that dilation promotes callus formation in the bone tunnel wall and prevents the complication of bone tunnel enlargement after ligament reconstruction

  15. A new version of the RDP (Ribosomal Database Project)

    Science.gov (United States)

    Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.; hide

    1999-01-01

    The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

  16. Ecologies of Ideologies : Explaining Party Entry and Exit in West-European Parliaments, 1945-2013

    NARCIS (Netherlands)

    van de Wardt, M.; Berkhout, J.; Vermeulen, F.

    2017-01-01

    This study introduces a population-ecological approach to the entry and exit of political parties. A primary proposition of population ecology is that organizational entry and exit depends on the number of organizations already present: that is, density. We propose that political parties mainly

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

    Science.gov (United States)

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

    2017-09-01

    Several groups of antibiotics inhibit bacterial growth by binding to bacterial ribosomes. Mutations in ribosomal protein L3 have been associated with resistance to linezolid and tiamulin, which both bind at the peptidyl transferase center in the ribosome. Resistance to these and other antibiotics also occurs through methylation of 23S rRNA at position A2503 by the methyltransferase Cfr. The mutations in L3 and the cfr gene have been found together in clinical isolates, raising the question of whether they have a combined effect on antibiotic resistance or growth. We transformed a plasmid-borne cfr gene into a uL3-depleted Escherichia coli strain containing either wild-type L3 or L3 with one of seven mutations, G147R, Q148F, N149S, N149D, N149R, Q150L, or T151P, expressed from plasmid-carried rplC genes. The L3 mutations are well tolerated, with small to moderate growth rate decreases. The presence of Cfr has a very minor influence on the growth rate. The resistance of the transformants to linezolid, tiamulin, florfenicol, and Synercid (a combination of quinupristin and dalfopristin [Q-D]) was measured by MIC assays. The resistance from Cfr was, in all cases, stronger than the effects of the L3 mutations, but various effects were obtained with the combinations of Cfr and L3 mutations ranging from a synergistic to an antagonistic effect. Linezolid and tiamulin susceptibility varied greatly among the L3 mutations, while no significant effects on florfenicol and Q-D susceptibility were seen. This study underscores the complex interplay between various resistance mechanisms and cross-resistance, even from antibiotics with overlapping binding sites. Copyright © 2017 American Society for Microbiology.

  18. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

    DEFF Research Database (Denmark)

    Villa, Elizabeth; Sengupta, Jayati; Trabuco, Leonard G.

    2009-01-01

    In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.......7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions...... of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic...

  19. Tunnel fire testing and modeling the Morgex North tunnel experiment

    CERN Document Server

    Borghetti, Fabio; Gandini, Paolo; Frassoldati, Alessio; Tavelli, Silvia

    2017-01-01

    This book aims to cast light on all aspects of tunnel fires, based on experimental activities and theoretical and computational fluid dynamics (CFD) analyses. In particular, the authors describe a transient full-scale fire test (~15 MW), explaining how they designed and performed the experimental activity inside the Morgex North tunnel in Italy. The entire organization of the experiment is described, from preliminary evaluations to the solutions found for management of operational difficulties and safety issues. This fire test allowed the collection of different measurements (temperature, air velocity, smoke composition, pollutant species) useful for validating and improving CFD codes and for testing the real behavior of the tunnel and its safety systems during a diesel oil fire with a significant heat release rate. Finally, the fire dynamics are compared with empirical correlations, CFD simulations, and literature measurements obtained in other similar tunnel fire tests. This book will be of interest to all ...

  20. Sampling for Patient Exit Interviews: Assessment of Methods Using Mathematical Derivation and Computer Simulations.

    Science.gov (United States)

    Geldsetzer, Pascal; Fink, Günther; Vaikath, Maria; Bärnighausen, Till

    2018-02-01

    (1) To evaluate the operational efficiency of various sampling methods for patient exit interviews; (2) to discuss under what circumstances each method yields an unbiased sample; and (3) to propose a new, operationally efficient, and unbiased sampling method. Literature review, mathematical derivation, and Monte Carlo simulations. Our simulations show that in patient exit interviews it is most operationally efficient if the interviewer, after completing an interview, selects the next patient exiting the clinical consultation. We demonstrate mathematically that this method yields a biased sample: patients who spend a longer time with the clinician are overrepresented. This bias can be removed by selecting the next patient who enters, rather than exits, the consultation room. We show that this sampling method is operationally more efficient than alternative methods (systematic and simple random sampling) in most primary health care settings. Under the assumption that the order in which patients enter the consultation room is unrelated to the length of time spent with the clinician and the interviewer, selecting the next patient entering the consultation room tends to be the operationally most efficient unbiased sampling method for patient exit interviews. © 2016 The Authors. Health Services Research published by Wiley Periodicals, Inc. on behalf of Health Research and Educational Trust.

  1. Optimization of a tunneling barrier in magnetic tunneling junction by tilted-plasma oxidation

    International Nuclear Information System (INIS)

    Nam, C.H.; Shim, Heejae; Kim, K.S.; Cho, B.K.

    2004-01-01

    Oxidation of an AlO x insulating barrier in a magnetic tunneling junction (MTJ) was carried out by a tilted-plasma oxidation method. It was found that the tilted-plasma oxidation induced a gradual change in the extent of oxidation of an insulating layer, which consequently led to a gradual change in the tunneling magnetoresistance (TMR) and specific junction resistance (RA) of the MTJ. We found a linear relation in the TMR versus RA curve with positive and negative slopes for less- and overoxidized junctions, respectively, and a parabolic relation for optimally oxidized junctions. The crossover in the TMR versus RA curves provides an effective and useful way to optimize (and monitor) the oxidation condition of a tunneling barrier in MTJs especially of a tunneling barrier less than 10 A thick. The tunneling junctions were also investigated after thermal annealing at various temperatures. The observations after thermal annealing were found to be consistent with transmission electrons microscopy images and a scenario of the partial formation of an additional ultrathin tunneling barrier at the top surface of the bottom magnetic layer

  2. Nuclear Export of Pre-Ribosomal Subunits Requires Dbp5, but Not as an RNA-Helicase as for mRNA Export.

    Science.gov (United States)

    Neumann, Bettina; Wu, Haijia; Hackmann, Alexandra; Krebber, Heike

    2016-01-01

    The DEAD-box RNA-helicase Dbp5/Rat8 is known for its function in nuclear mRNA export, where it displaces the export receptor Mex67 from the mRNA at the cytoplasmic side of the nuclear pore complex (NPC). Here we show that Dbp5 is also required for the nuclear export of both pre-ribosomal subunits. Yeast temperature-sensitive dbp5 mutants accumulate both ribosomal particles in their nuclei. Furthermore, Dbp5 genetically and physically interacts with known ribosomal transport factors such as Nmd3. Similar to mRNA export we show that also for ribosomal transport Dbp5 is required at the cytoplasmic side of the NPC. However, unlike its role in mRNA export, Dbp5 does not seem to undergo its ATPase cycle for this function, as ATPase-deficient dbp5 mutants that selectively inhibit mRNA export do not affect ribosomal transport. Furthermore, mutants of GLE1, the ATPase stimulating factor of Dbp5, show no major ribosomal export defects. Consequently, while Dbp5 uses its ATPase cycle to displace the export receptor Mex67 from the translocated mRNAs, Mex67 remains bound to ribosomal subunits upon transit to the cytoplasm, where it is detectable on translating ribosomes. Therefore, we propose a model, in which Dbp5 supports ribosomal transport by capturing ribosomal subunits upon their cytoplasmic appearance at the NPC, possibly by binding export factors such as Mex67. Thus, our findings reveal that although different ribonucleoparticles, mRNAs and pre-ribosomal subunits, use shared export factors, they utilize different transport mechanisms.

  3. Pactamycin binding site on archaebacterial and eukaryotic ribosomes

    International Nuclear Information System (INIS)

    Tejedor, F.; Amils, R.; Ballesta, J.P.G.

    1987-01-01

    The presence of a photoreactive acetophenone group in the protein synthesis inhibitor pactamycin and the possibility of obtaining active iodinated derivatives that retain full biological activity allow the antibiotic binding site on Saccharomyces cerevisiae and archaebacterium Sulfolobus solfataricus ribosomes to be photoaffinity labeled. Four major labeled proteins have been identified in the yeast ribosomes, i.e., YS10, YS18, YS21/24, and YS30, while proteins AL1a, AS10/L8, AS18/20, and AS21/22 appeared as radioactive spots in S. solfataricus. There seems to be a correlation between some of the proteins labeled in yeast and those previously reported in Escherichia coli indicating that the pactamycin binding sites of both species, which are in the small subunit close to the initiation factors and mRNA binding sites, must have similar characteristics

  4. Ribosome-catalyzed formation of an abnormal peptide analogue

    International Nuclear Information System (INIS)

    Roesser, J.R.; Chorghade, M.S.; Hecht, S.M.

    1986-01-01

    The peptidyl-tRNA analogue N-(chloracetyl) phenylalanyl-tRNA/sup Phe/ was prepared by chemical aminoacylation and prebound to the P site of Escherichia coli ribosomes in response to poly(uridylic acid). Admixture of phenylalanyl-tRNA/sup Phe/ to the A site resulted in the formation of two dipeptides, one of which was found by displacement of chloride ion from the peptidyl-tRNA. This constitutes the first example of ribosome-mediated formation of a peptide of altered connectivity and suggests a need for revision of the current model of peptide bond formation. Also suggested by the present finding is the feasibility of utilizing tRNAs to prepare polypeptides of altered connectivity in an in vitro protein biosynthesizing system. [ 32 P]-oligo(rA), [ 3 H]- and [ 14 C] phenylalanines were used in the assay of the peptidye-tRNA analogue

  5. Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome.

    Science.gov (United States)

    Sharma, Divya; Cukras, Anthony R; Rogers, Elizabeth J; Southworth, Daniel R; Green, Rachel

    2007-12-07

    The fidelity of aminoacyl-tRNA selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-tRNA. The aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. Structural and biochemical studies have identified ribosomal protein S12 (as well as specific nucleotides in 16S ribosomal RNA) as a critical molecular contributor in distinguishing between cognate and near-cognate tRNA species as well as in promoting more global rearrangements in the small subunit, referred to as "closure." Here we use a mutational approach to define contributions made by two highly conserved loops in S12 to the process of tRNA selection. Most S12 variant ribosomes tested display increased levels of fidelity (a "restrictive" phenotype). Interestingly, several variants, K42A and R53A, were substantially resistant to the miscoding effects of paromomycin. Further characterization of the compromised paromomycin response identified a probable second, fidelity-modulating binding site for paromomycin in the 16S ribosomal RNA that facilitates closure of the small subunit and compensates for defects associated with the S12 mutations.

  6. Quantum mechanical tunneling in chemical physics

    CERN Document Server

    Nakamura, Hiroki

    2016-01-01

    Quantum mechanical tunneling plays important roles in a wide range of natural sciences, from nuclear and solid-state physics to proton transfer and chemical reactions in chemistry and biology. Responding to the need for further understanding of multidimensional tunneling, the authors have recently developed practical methods that can be applied to multidimensional systems. Quantum Mechanical Tunneling in Chemical Physics presents basic theories, as well as original ones developed by the authors. It also provides methodologies and numerical applications to real molecular systems. The book offers information so readers can understand the basic concepts and dynamics of multidimensional tunneling phenomena and use the described methods for various molecular spectroscopy and chemical dynamics problems. The text focuses on three tunneling phenomena: (1) energy splitting, or tunneling splitting, in symmetric double well potential, (2) decay of metastable state through tunneling, and (3) tunneling effects in chemical...

  7. Tunneling into quantum wires: regularization of the tunneling Hamiltonian and consistency between free and bosonized fermions

    OpenAIRE

    Filippone, Michele; Brouwer, Piet

    2016-01-01

    Tunneling between a point contact and a one-dimensional wire is usually described with the help of a tunneling Hamiltonian that contains a delta function in position space. Whereas the leading order contribution to the tunneling current is independent of the way this delta function is regularized, higher-order corrections with respect to the tunneling amplitude are known to depend on the regularization. Instead of regularizing the delta function in the tunneling Hamiltonian, one may also obta...

  8. The Potential of Targeting Ribosome Biogenesis in High-Grade Serous Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Shunfei Yan

    2017-01-01

    Full Text Available Overall survival for patients with ovarian cancer (OC has shown little improvement for decades meaning new therapeutic options are critical. OC comprises multiple histological subtypes, of which the most common and aggressive subtype is high-grade serous ovarian cancer (HGSOC. HGSOC is characterized by genomic structural variations with relatively few recurrent somatic mutations or dominantly acting oncogenes that can be targeted for the development of novel therapies. However, deregulation of pathways controlling homologous recombination (HR and ribosome biogenesis has been observed in a high proportion of HGSOC, raising the possibility that targeting these basic cellular processes may provide improved patient outcomes. The poly (ADP-ribose polymerase (PARP inhibitor olaparib has been approved to treat women with defects in HR due to germline BRCA mutations. Recent evidence demonstrated the efficacy of targeting ribosome biogenesis with the specific inhibitor of ribosomal RNA synthesis, CX-5461 in v-myc avian myelocytomatosis viral oncogene homolog (MYC-driven haematological and prostate cancers. CX-5461 has now progressed to a phase I clinical trial in patients with haematological malignancies and phase I/II trial in breast cancer. Here we review the currently available targeted therapies for HGSOC and discuss the potential of targeting ribosome biogenesis as a novel therapeutic approach against HGSOC.

  9. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

    Science.gov (United States)

    Herbert, Zachary T; Kershner, Jamie P; Butty, Vincent L; Thimmapuram, Jyothi; Choudhari, Sulbha; Alekseyev, Yuriy O; Fan, Jun; Podnar, Jessica W; Wilcox, Edward; Gipson, Jenny; Gillaspy, Allison; Jepsen, Kristen; BonDurant, Sandra Splinter; Morris, Krystalynne; Berkeley, Maura; LeClerc, Ashley; Simpson, Stephen D; Sommerville, Gary; Grimmett, Leslie; Adams, Marie; Levine, Stuart S

    2018-03-15

    Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

  10. Tunnelling of a molecule

    International Nuclear Information System (INIS)

    Jarvis, P.D.; Bulte, D.P.

    1998-01-01

    A quantum-mechanical description of tunnelling is presented for a one-dimensional system with internal oscillator degrees of freedom. The 'charged diatomic molecule' is frustrated on encountering a barrier potential by its centre of charge not being coincident with its centre of mass, resulting in transitions amongst internal states. In an adiabatic limit, the tunnelling of semiclassical coherent-like oscillator states is shown to exhibit the Hartman and Bueuttiker-Landauer times t H and t BL , with the time dependence of the coherent state parameter for the tunnelled state given by α(t) = α e -iω(t+Δt) , Δt = t H - it BL . A perturbation formalism is developed, whereby the exact transfer matrix can be expanded to any desired accuracy in a suitable limit. An 'intrinsic' time, based on the oscillator transition rate during tunnelling, transmission or reflection, is introduced. In simple situations the resulting intrinsic tunnelling time is shown to vanish to lowest order. In the general case a particular (nonzero) parametrisation is inferred, and its properties discussed in comparison with the literature on tunnelling times for both wavepackets and internal clocks. Copyright (1998) CSIRO Australia

  11. The exit-time problem for a Markov jump process

    Science.gov (United States)

    Burch, N.; D'Elia, M.; Lehoucq, R. B.

    2014-12-01

    The purpose of this paper is to consider the exit-time problem for a finite-range Markov jump process, i.e, the distance the particle can jump is bounded independent of its location. Such jump diffusions are expedient models for anomalous transport exhibiting super-diffusion or nonstandard normal diffusion. We refer to the associated deterministic equation as a volume-constrained nonlocal diffusion equation. The volume constraint is the nonlocal analogue of a boundary condition necessary to demonstrate that the nonlocal diffusion equation is well-posed and is consistent with the jump process. A critical aspect of the analysis is a variational formulation and a recently developed nonlocal vector calculus. This calculus allows us to pose nonlocal backward and forward Kolmogorov equations, the former equation granting the various moments of the exit-time distribution.

  12. Influence of quasiparticle multi-tunneling on the energy flow through the superconducting tunnel junction

    International Nuclear Information System (INIS)

    Samedov, V. V.; Tulinov, B. M.

    2011-01-01

    Superconducting tunnel junction (STJ) detector consists of two layers of superconducting material separated by thin insulating barrier. An incident particle produces in superconductor excess nonequilibrium quasiparticles. Each quasiparticle in superconductor should be considered as quantum superposition of electron-like and hole-like excitations. This duality nature of quasiparticle leads to the effect of multi-tunneling. Quasiparticle starts to tunnel back and forth through the insulating barrier. After tunneling from biased electrode quasiparticle loses its energy via phonon emission. Eventually, the energy that equals to the difference in quasiparticle energy between two electrodes is deposited in the signal electrode. Because of the process of multi-tunneling, one quasiparticle can deposit energy more than once. In this work, the theory of branching cascade processes was applied to the process of energy deposition caused by the quasiparticle multi-tunneling. The formulae for the mean value and variance of the energy transferred by one quasiparticle into heat were derived. (authors)

  13. Enhanced MRI in carpal tunnel syndrome

    International Nuclear Information System (INIS)

    Hayakawa, Katsuhiko; Nakane, Takashi; Kobayashi, Shigeru; Asai, Takahiro; Wada, Kunio; Yoshizawa, Hidezo

    1998-01-01

    In this study, we performed contrast-enhanced MRI in patients with idiopathic carpal tunnel syndrome and examined the morphologic change in the carpal tunnel. In the transverse section of the opening of carpal tunnel where scaphoid and pisiform bones are figured out, we measured and examined 4 items, viz. the soft carpal tunnel volume, flat rate of median nerve, position of median nerve and thickness of palmer ligaments composing the base of carpal tunnel, with an image analyzer attached to the MRI apparatus. Whereas the average carpal tunnel volume in 12 hands of normal controls was 166.8 mm 2 , that in 74 hands of carpal tunnel syndrome was 207.2 mm 2 , a significant increase compared with the normal controls. The flat rate of median nerve was 46% in the controls, but that was 37.5% in the carpal tunnel syndrome, a significant flattening was noted. We connected the peaks of the scaphoid node and pisiform bone with a line and named it standard line. When we observed the position of median nerve in the carpal tunnel, the nerve in 9 of 12 hands, 75%, lay below the standard line in the controls, but the nerve in 65 of 74 hands, 87.8%, lay above the standard line in the carpal tunnel syndrome, clearly showing that the median nerve had shifted to the palmar side. Regarding these morphologic changes of the carpal tunnel, the internal pressure of the carpal tunnel is considered to be raised with swelling of the soft tissues mainly composing the inside of carpal tunnel, thus the area of cross section of carpal tunnel to be increased, the median nerve to be shifted to the palmar side and the median nerve to be compressed by the transverse carpal ligament at that time. Although we can observe these morphological changes readily in MRI images, these images show only the results of carpal tunnel syndrome after all, and do not specify the direct causes. However, we believe that these facts are important factors in the manifestation of idiopathic carpal tunnel syndrome. (author)

  14. Josephson tunneling and nanosystems

    OpenAIRE

    Ovchinnikov, Yurii; Kresin, Vladimir

    2010-01-01

    Josephson tunneling between nanoclusters is analyzed. The discrete nature of the electronic energy spectra, including their shell ordering, is explicitly taken into account. The treatment considers the two distinct cases of resonant and non-resonant tunneling. It is demonstrated that the current density greatly exceeds the value discussed in the conventional theory. Nanoparticles are shown to be promising building blocks for nanomaterials-based tunneling networks.

  15. Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.

    Science.gov (United States)

    Hulscher, Ryan M; Bohon, Jen; Rappé, Mollie C; Gupta, Sayan; D'Mello, Rhijuta; Sullivan, Michael; Ralston, Corie Y; Chance, Mark R; Woodson, Sarah A

    2016-07-01

    The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

    Science.gov (United States)

    Meilijson, Isaac; Kupiec, Martin; Ruppin, Eytan

    2011-01-01

    We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance levels, ribosomal densities and the relation between all these variables, better than alternative (‘non-physical’) approaches. In addition, we show that the RFM can be used for accurate inference of various other quantities including genes' initiation rates and translation costs. These quantities could not be inferred by previous predictors. We find that increasing the number of available ribosomes (or equivalently the initiation rate) increases the genomic translation rate and the mean ribosome density only up to a certain point, beyond which both saturate. Strikingly, assuming that the translation system is tuned to work at the pre-saturation point maximizes the predictive power of the model with respect to experimental data. This result suggests that in all organisms that were analyzed (from bacteria to Human), the global initiation rate is optimized to attain the pre-saturation point. The fact that similar results were not observed for heterologous genes indicates that this feature is under selection. Remarkably, the gap between the performance of the RFM and alternative predictors is strikingly large in the case of heterologous genes, testifying to the model's promising biotechnological value in predicting the abundance of heterologous proteins before expressing them in the desired host. PMID:21909250

  17. Probing spin-polarized tunneling at high bias and temperature with a magnetic tunnel transistor

    NARCIS (Netherlands)

    Park, B.G.; Banerjee, T.; Min, B.C.; Sanderink, Johannes G.M.; Lodder, J.C.; Jansen, R.

    2005-01-01

    The magnetic tunnel transistor (MTT) is a three terminal hybrid device that consists of a tunnel emitter, a ferromagnetic (FM) base, and a semiconductor collector. In the MTT with a FM emitter and a single FM base, spin-polarized hot electrons are injected into the base by tunneling. After

  18. Control of tunneling in heterostructures

    International Nuclear Information System (INIS)

    Volokhov, V M; Tovstun, C A; Ivlev, B

    2007-01-01

    A tunneling current between two rectangular potential wells can be effectively controlled by applying an external ac field. A variation of the ac frequency by 10% may lead to the suppression of the tunneling current by two orders of magnitude, which is a result of quantum interference under the action of the ac field. This effect of destruction of tunneling can be used as a sensitive control of tunneling current across nanosize heterostructures

  19. Cross-linking of streptomycin to the 16S ribosomal RNA of Escherichia coli

    International Nuclear Information System (INIS)

    Gravel, M.; Melancon, P.; Barkier-Gingras, L.

    1987-01-01

    [ 3 H]Dihydrostreptomycin was cross-linked to the 30S ribosomal subunit from Escherichia coli with the bifunctional reagent nitrogen mustard. The cross-linking primarily involved the 16S RNA. To localize the site of cross-linking of streptomycin to the 16S RNA, the authors hybridized RNA labeled with streptomycin to restriction fragments of the 16S RNA gene. Labeled RNA hybridized to DNA fragments corresponding to bases 892-917 and bases 1394-1415. These two segments of the ribosomal RNA must by juxtaposed in the ribosome, since there is a single binding site for streptomycin. This region has been implicated both in the decoding site and in the binding of initiation factor IF-3, indicating its functional importance

  20. In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin.

    Science.gov (United States)

    Sidhu, Amar Bir Singh; Sun, Qingan; Nkrumah, Louis J; Dunne, Michael W; Sacchettini, James C; Fidock, David A

    2007-01-26

    Azithromycin (AZ), a broad-spectrum antibacterial macrolide that inhibits protein synthesis, also manifests reasonable efficacy as an antimalarial. Its mode of action against malarial parasites, however, has remained undefined. Our in vitro investigations with the human malarial parasite Plasmodium falciparum document a remarkable increase in AZ potency when exposure is prolonged from one to two generations of intraerythrocytic growth, with AZ producing 50% inhibition of parasite growth at concentrations in the mid to low nanomolar range. In our culture-adapted lines, AZ displayed no synergy with chloroquine (CQ), amodiaquine, or artesunate. AZ activity was also unaffected by mutations in the pfcrt (P. falciparum chloroquine resistance transporter) or pfmdr1 (P. falciparum multidrug resistance-1) drug resistance loci, as determined using transgenic lines. We have selected mutant, AZ-resistant 7G8 and Dd2 parasite lines. In the AZ-resistant 7G8 line, the bacterial-like apicoplast large subunit ribosomal RNA harbored a U438C mutation in domain I. Both AZ-resistant lines revealed a G76V mutation in a conserved region of the apicoplast-encoded P. falciparum ribosomal protein L4 (PfRpl4). This protein is predicted to associate with the nuclear genome-encoded P. falciparum ribosomal protein L22 (PfRpl22) and the large subunit rRNA to form the 50 S ribosome polypeptide exit tunnel that can be occupied by AZ. The PfRpl22 sequence remained unchanged. Molecular modeling of mutant PfRpl4 with AZ suggests an altered orientation of the L75 side chain that could preclude AZ binding. These data imply that AZ acts on the apicoplast bacterial-like translation machinery and identify Pfrpl4 as a potential marker of resistance.

  1. Origins of the plant chloroplasts and mitochondria based on comparisons of 5S ribosomal RNAs

    Science.gov (United States)

    Delihas, N.; Fox, G. E.

    1987-01-01

    In this paper, we provide macromolecular comparisons utilizing the 5S ribosomal RNA structure to suggest extant bacteria that are the likely descendants of chloroplast and mitochondria endosymbionts. The genetic stability and near universality of the 5S ribosomal gene allows for a useful means to study ancient evolutionary changes by macromolecular comparisons. The value in current and future ribosomal RNA comparisons is in fine tuning the assignment of ancestors to the organelles and in establishing extant species likely to be descendants of bacteria involved in presumed multiple endosymbiotic events.

  2. Tunnelling in Soft Soil : Tunnel Boring Machine Operation and Soil Response

    NARCIS (Netherlands)

    Festa, D.; Broere, W.; Bosch, J.W.

    2013-01-01

    Constructing tunnels in soft soil with the use of Tunnel Boring Machines may induce settlements including soil movements ahead of the face, soil relaxation into the tail void, possible heave due to grouting, long lasting consolidation processes, and potentially several other mechanisms. A

  3. Plastid ribosome pausing is induced by multiple features and is linked to protein complex assembly

    DEFF Research Database (Denmark)

    Gawroński, Piotr; Jensen, Poul Erik; Karpinski, Stanislaw

    2018-01-01

    Many mRNAs contain pause sites that briefly interrupt the progress of translation. Specific features that induce ribosome pausing have been described; however, their individual contributions to pause-site formation, and the overall biological significance of ribosome pausing, remain largely uncle...

  4. Seismic prediction ahead of tunnel constructions

    Science.gov (United States)

    Jetschny, S.; Bohlen, T.; Nil, D. D.; Giese, R.

    2007-12-01

    To increase safety and efficiency of tunnel constructions, online seismic exploration ahead of a tunnel can become a valuable tool. Within the \\it OnSite project founded by the BMBF (German Ministry of Education and Research) within \\it GeoTechnologien a new forward looking seismic imaging technique is developed to e.g. determine weak and water bearing zones ahead of the constructions. Our approach is based on the excitation and registration of \\it tunnel surface waves. These waves are excited at the tunnel face behind the cutter head of a tunnel boring machine and travel into drilling direction. Arriving at the front face they generate body waves (mainly S-waves) propagating further ahead. Reflected S-waves are back- converted into tunnel surface waves. For a theoretical description of the conversion process and for finding optimal acquisition geometries it is of importance to study the propagation characteristics of tunnel surface waves. 3D seismic finite difference modeling and analytic solutions of the wave equation in cylindric coordinates revealed that at higher frequencies, i.e. if the tunnel diameter is significantly larger than the wavelength of S-waves, these surface waves can be regarded as Rayleigh-waves circulating the tunnel. For smaller frequencies, i.e. when the S-wavelength approaches the tunnel diameter, the propagation characteristics of these surface waves are then similar to S- waves. Field measurements performed by the GeoForschungsZentrum Potsdam, Germany at the Gotthard Base Tunnel (Switzerland) show both effects, i.e. the propagation of Rayleigh- and body-wave like waves along the tunnel. To enhance our understanding of the excitation and propagation characteristics of tunnel surface waves the transition of Rayleigh to tube-waves waves is investigated both analytically and by numerical simulations.

  5. Probability evolution method for exit location distribution

    Science.gov (United States)

    Zhu, Jinjie; Chen, Zhen; Liu, Xianbin

    2018-03-01

    The exit problem in the framework of the large deviation theory has been a hot topic in the past few decades. The most probable escape path in the weak-noise limit has been clarified by the Freidlin-Wentzell action functional. However, noise in real physical systems cannot be arbitrarily small while noise with finite strength may induce nontrivial phenomena, such as noise-induced shift and noise-induced saddle-point avoidance. Traditional Monte Carlo simulation of noise-induced escape will take exponentially large time as noise approaches zero. The majority of the time is wasted on the uninteresting wandering around the attractors. In this paper, a new method is proposed to decrease the escape simulation time by an exponentially large factor by introducing a series of interfaces and by applying the reinjection on them. This method can be used to calculate the exit location distribution. It is verified by examining two classical examples and is compared with theoretical predictions. The results show that the method performs well for weak noise while may induce certain deviations for large noise. Finally, some possible ways to improve our method are discussed.

  6. Histopathological detection of entry and exit holes in human skin wounds caused by firearms.

    Science.gov (United States)

    Baptista, Marcus Vinícius; d'Ávila, Solange C G P; d'Ávila, Antônio Miguel M P

    2014-07-01

    The judiciary needs forensic medicine to determine the difference between an entry hole and an exit hole in human skin caused by firearms for civilian use. This important information would be most useful if a practical and accurate method could be done with low-cost and minimal technological resources. Both macroscopic and microscopic analyses were performed on skin lesions caused by firearm projectiles, to establish histological features of 14 entry holes and 14 exit holes. Microscopically, in the abrasion area macroscopically observed, there were signs of burns (sub-epidermal cracks and keratinocyte necrosis) in the entrance holes in all cases. These signs were not found in three exit holes which showed an abrasion collar, nor in other exit holes. Some other microscopic features not found in every case were limited either to entry holes, such as cotton fibres, grease deposits, or tattooing in the dermis, or to exit holes, such as adipose tissue, bone or muscle tissue in the dermis. Coagulative necrosis of keratinocytes and sub-epidermal cracks are characteristic of entry holes. Despite the small sample size, it can be safely inferred that this is an important microscopic finding, among others less consistently found, to define an entry hole in questionable cases. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  7. Gap anisotropy and tunneling currents. [MPS3

    DEFF Research Database (Denmark)

    Lazarides, N.; Sørensen, Mads Peter

    1996-01-01

    The tunneling Hamiltonian formalism is applied to calculate the tunnelingcurrents through a small superconducting tunnel junction. The formalism isextended to nonconstant tunneling matrix elements. The electrodes of thejunction are assumed to......The tunneling Hamiltonian formalism is applied to calculate the tunnelingcurrents through a small superconducting tunnel junction. The formalism isextended to nonconstant tunneling matrix elements. The electrodes of thejunction are assumed to...

  8. Exit and Failure of Credit Unions in Brazil: A Risk Analysis

    Directory of Open Access Journals (Sweden)

    Flávio Leonel de Carvalho

    2015-04-01

    Full Text Available This study aims to investigate the factors that affect the market exit of Brazilian singular credit unions from 1995 to 2009; it also identifies and lists the determinants of various types of market exits and analyzes whether profitability is a significant factor for credit union survival. This study was conducted with accounting data provided by the Central Bank of Brazil, which derives only from individual cooperatives, i.e. singular credit unions. Quarterly financial statements from these credit unions that were active from 1995 to the second quarter of 2009 were employed, totaling 71,325 observations for 1,929 credit unions. Based on survival and the model of competing risks (such as the Cox, Exponential, Weibull, Gompertz, and Competing Risk models, the results show that there is no statistical evidence to ensure a correlation between profitability and credit union survival. The results also suggest that the size of credit unions plays a key role in their survival and longevity and that their funding and investment management are related to their survival and risk of market exit. In conclusion, the results confirm the initial idea that the duality inherent to credit unions - cooperative principles versus economic efficiency - might influence the stability, survival, and longevity of these institutions. Such results may also imply that a credit union embracing the rationale of a private bank will become more estranged from its members, something which will hinder its future operations and increase the likelihood of its exit from the market.

  9. Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA.

    Science.gov (United States)

    Hochstatter, Julia; Hölzel, Michael; Rohrmoser, Michaela; Schermelleh, Lothar; Leonhardt, Heinrich; Keough, Rebecca; Gonda, Thomas J; Imhof, Axel; Eick, Dirk; Längst, Gernot; Németh, Attila

    2012-07-13

    Ribosomal RNA gene transcription, co-transcriptional processing, and ribosome biogenesis are highly coordinated processes that are tightly regulated during cell growth. In this study we discovered that Mybbp1a is associated with both the RNA polymerase I complex and the ribosome biogenesis machinery. Using a reporter assay that uncouples transcription and RNA processing, we show that Mybbp1a represses rRNA gene transcription. In addition, overexpression of the protein reduces RNA polymerase I loading on endogenous rRNA genes as revealed by chromatin immunoprecipitation experiments. Accordingly, depletion of Mybbp1a results in an accumulation of the rRNA precursor in vivo but surprisingly also causes growth arrest of the cells. This effect can be explained by the observation that the modulation of Mybbp1a protein levels results in defects in pre-rRNA processing within the cell. Therefore, the protein may play a dual role in the rRNA metabolism, potentially linking and coordinating ribosomal DNA transcription and pre-rRNA processing to allow for the efficient synthesis of ribosomes.

  10. Magnetic Fluxtube Tunneling

    Science.gov (United States)

    Dahlburg, Russell B.; Antiochos,, Spiro K.; Norton, D.

    1996-01-01

    We present numerical simulations of the collision and subsequent interaction of two initially orthogonal, twisted, force free field magnetic fluxtubes. The simulations were carried out using a new three dimensional explicit parallelized Fourier collocation algorithm for solving the viscoresistive equations of compressible magnetohydrodynamics. It is found that, under a wide range of conditions, the fluxtubes can 'tunnel' through each other. Two key conditions must be satisfied for tunneling to occur: the magnetic field must be highly twisted with a field line pitch much greater than 1, and the magnetic Lundquist number must be somewhat large, greater than or equal to 2880. This tunneling behavior has not been seen previously in studies of either vortex tube or magnetic fluxtube interactions. An examination of magnetic field lines shows that tunneling is due to a double reconnection mechanism. Initially orthogonal field lines reconnect at two specific locations, exchange interacting sections and 'pass' through each other. The implications of these results for solar and space plasmas are discussed.

  11. Kinase-Mediated Regulation of 40S Ribosome Assembly in Human Breast Cancer

    Science.gov (United States)

    2017-02-01

    and will assess if this resistance involves gain-of-function mutations in Ltv1, and if resistance can be overcome with drugs that direct...ribosome assembly factor Ltv1 in both yeast and TNBC cells, and that selective knockdown or silencing of CK1δ, or forced expression of Ltv1 mutant that...cannot be phosphorylated by CK1δ, blocks ribosome assembly in yeast and compromises the growth and survival of TNBC cells. Further, we have shown that

  12. The Ribosomal RNA is a Useful Marker to Visualize Rhizobia Interacting with Legume Plants

    Science.gov (United States)

    Rinaudi, Luciana; Isola, Maria C.; Giordano, Walter

    2004-01-01

    Symbiosis between rhizobia and leguminous plants leads to the formation of nitrogen-fixing root nodules. In the present article, we recommend the use of the ribosomal RNA (rRNA) isolated from legume nodules in an experimental class with the purpose of introducing students to the structure of eukaryotic and prokaryotic ribosomes and of…

  13. Atomistic modeling trap-assisted tunneling in hole tunnel field effect transistors

    Science.gov (United States)

    Long, Pengyu; Huang, Jun Z.; Povolotskyi, Michael; Sarangapani, Prasad; Valencia-Zapata, Gustavo A.; Kubis, Tillmann; Rodwell, Mark J. W.; Klimeck, Gerhard

    2018-05-01

    Tunnel Field Effect Transistors (FETs) have the potential to achieve steep Subthreshold Swing (S.S.) below 60 mV/dec, but their S.S. could be limited by trap-assisted tunneling (TAT) due to interface traps. In this paper, the effect of trap energy and location on OFF-current (IOFF) of tunnel FETs is evaluated systematically using an atomistic trap level representation in a full quantum transport simulation. Trap energy levels close to band edges cause the highest leakage. Wave function penetration into the surrounding oxide increases the TAT current. To estimate the effects of multiple traps, we assume that the traps themselves do not interact with each other and as a whole do not modify the electrostatic potential dramatically. Within that model limitation, this numerical metrology study points to the critical importance of TAT in the IOFF in tunnel FETs. The model shows that for Dit higher than 1012/(cm2 eV) IO F F is critically increased with a degraded IO N/IO F F ratio of the tunnel FET. In order to have an IO N/IO F F ratio higher than 104, the acceptable Dit near Ev should be controlled to no larger than 1012/(cm2 eV) .

  14. Fast Water Transport in CNTs: length dependence and entrane/exit effects

    DEFF Research Database (Denmark)

    Walther, Jens Honore; Koumoutsakos, Petros

    Superfast water transport in carbon nanotube (CNT) membranes has been reported in experimental studies. We use Molecular Dynamics simulations to elucidate the mechanisms of water entry, exit and transport in 2nm-diameter hydrophobic CNTs embedded in a hydrophilic membrane matrix. We demonstrate......, for the first time, that under imposed pressures of the order of 1 bar, water entry into the CNT cavity and exit from the CNT end, can occur only on pre-wetted membranes. We conduct large scale simulations for up to 500nm long CNTs and observe a previously unseen dependence of the flow enhancement rates...

  15. Forthcoming EU Rules on Exit Taxes for Companies

    NARCIS (Netherlands)

    van de Streek, J.

    2015-01-01

    Rules on exit taxation for the EU as a whole are under construction at European Council level. Formally, the work on this piece of EU tax legislation is part of the controversial Common Consolidated Corporate Tax Base (CCCTB). But it is also thinkable that even without a CCCTB being established in

  16. Lowest order in inelastic tunneling approximation : efficient scheme for simulation of inelastic electron tunneling data

    NARCIS (Netherlands)

    Rossen, E.T.R.; Flipse, C.F.J.; Cerda, J.I.

    2013-01-01

    We have developed an efficient and accurate formalism which allows the simulation at the ab initio level of inelastic electron tunneling spectroscopy data under a scanning tunneling microscope setup. It exploits fully the tunneling regime by carrying out the structural optimization and vibrational

  17. Scanning tunneling microscopic images and scanning tunneling spectra for coupled rectangular quantum corrals

    International Nuclear Information System (INIS)

    Mitsuoka, Shigenori; Tamura, Akira

    2011-01-01

    Assuming that an electron confined by double δ-function barriers lies in a quasi-stationary state, we derived eigenstates and eigenenergies of the electron. Such an electron has a complex eigenenergy, and the imaginary part naturally leads to the lifetime of the electron associated with tunneling through barriers. We applied this point of view to the electron confined in a rectangular quantum corral (QC) on a noble metal surface, and obtained scanning tunneling microscopic images and a scanning tunneling spectrum consistent with experimental ones. We investigated the electron states confined in coupled QCs and obtained the coupled states constructed with bonding and anti-bonding states. Using those energy levels and wavefunctions we specified scanning tunneling microscope (STM) images and scanning tunneling spectra (STS) for the doubly and triply coupled QCs. In addition we pointed out the feature of resonant electron states associated with the same QCs at both ends of the triply coupled QCs.

  18. Customer Protest: Exit, Voice or Negative Word of Mouth

    Directory of Open Access Journals (Sweden)

    Solvang, B. K.

    2008-01-01

    Full Text Available Of the three forms of protest the propensity of word of mouth (WOM seems to be the most common, and the most exclusive form of protest seems to be exit. The propensity for voice lies in between. The costs linked to voice influence the propensity for WOM. The customers seem to do an evaluation between the three forms of protest, yet the rational picture of the customers should be moderated.Leaders should improve their treatment of the customers making complaints. The more they can treat customer complaints in an orderly and nice way the less informal negative word of mouth activity they will experience and they will reduce the exit propensity and lead the customers to the complain organisation. They should also ensure that their customers feel they get equal treatment by the staff.

  19. Ivar Giaever, Tunneling, and Superconductors

    Science.gov (United States)

    dropdown arrow Site Map A-Z Index Menu Synopsis Ivar Giaever, Tunneling, and Superconductors Resources with in Superconductors Measured by Electron Tunneling; Physical Review Letters, Vol. 5 Issue 4: 147 - 148 ; August 15, 1960 Electron Tunneling Between Two Superconductors; Physical Review Letters, Vol. 5 Issue 10

  20. Physics of optimal resonant tunneling

    NARCIS (Netherlands)

    Racec, P.N.; Stoica, T.; Popescu, C.; Lepsa, M.I.; Roer, van de T.G.

    1997-01-01

    The optimal resonant tunneling, or the complete tunneling transparence of a biased double-barrier resonant-tunneling (DBRT) structure, is discussed. It is shown that its physics does not rest on the departure from the constant potential within the barriers and well, due to the applied electric

  1. The molecular chaperone Hsp90 is required for cell cycle exit in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Jennifer L Bandura

    Full Text Available The coordination of cell proliferation and differentiation is crucial for proper development. In particular, robust mechanisms exist to ensure that cells permanently exit the cell cycle upon terminal differentiation, and these include restraining the activities of both the E2F/DP transcription factor and Cyclin/Cdk kinases. However, the full complement of mechanisms necessary to restrain E2F/DP and Cyclin/Cdk activities in differentiating cells are not known. Here, we have performed a genetic screen in Drosophila melanogaster, designed to identify genes required for cell cycle exit. This screen utilized a PCNA-miniwhite(+ reporter that is highly E2F-responsive and results in a darker red eye color when crossed into genetic backgrounds that delay cell cycle exit. Mutation of Hsp83, the Drosophila homolog of mammalian Hsp90, results in increased E2F-dependent transcription and ectopic cell proliferation in pupal tissues at a time when neighboring wild-type cells are postmitotic. Further, these Hsp83 mutant cells have increased Cyclin/Cdk activity and accumulate proteins normally targeted for proteolysis by the anaphase-promoting complex/cyclosome (APC/C, suggesting that APC/C function is inhibited. Indeed, reducing the gene dosage of an inhibitor of Cdh1/Fzr, an activating subunit of the APC/C that is required for timely cell cycle exit, can genetically suppress the Hsp83 cell cycle exit phenotype. Based on these data, we propose that Cdh1/Fzr is a client protein of Hsp83. Our results reveal that Hsp83 plays a heretofore unappreciated role in promoting APC/C function during cell cycle exit and suggest a mechanism by which Hsp90 inhibition could promote genomic instability and carcinogenesis.

  2. The molecular chaperone Hsp90 is required for cell cycle exit in Drosophila melanogaster.

    Science.gov (United States)

    Bandura, Jennifer L; Jiang, Huaqi; Nickerson, Derek W; Edgar, Bruce A

    2013-01-01

    The coordination of cell proliferation and differentiation is crucial for proper development. In particular, robust mechanisms exist to ensure that cells permanently exit the cell cycle upon terminal differentiation, and these include restraining the activities of both the E2F/DP transcription factor and Cyclin/Cdk kinases. However, the full complement of mechanisms necessary to restrain E2F/DP and Cyclin/Cdk activities in differentiating cells are not known. Here, we have performed a genetic screen in Drosophila melanogaster, designed to identify genes required for cell cycle exit. This screen utilized a PCNA-miniwhite(+) reporter that is highly E2F-responsive and results in a darker red eye color when crossed into genetic backgrounds that delay cell cycle exit. Mutation of Hsp83, the Drosophila homolog of mammalian Hsp90, results in increased E2F-dependent transcription and ectopic cell proliferation in pupal tissues at a time when neighboring wild-type cells are postmitotic. Further, these Hsp83 mutant cells have increased Cyclin/Cdk activity and accumulate proteins normally targeted for proteolysis by the anaphase-promoting complex/cyclosome (APC/C), suggesting that APC/C function is inhibited. Indeed, reducing the gene dosage of an inhibitor of Cdh1/Fzr, an activating subunit of the APC/C that is required for timely cell cycle exit, can genetically suppress the Hsp83 cell cycle exit phenotype. Based on these data, we propose that Cdh1/Fzr is a client protein of Hsp83. Our results reveal that Hsp83 plays a heretofore unappreciated role in promoting APC/C function during cell cycle exit and suggest a mechanism by which Hsp90 inhibition could promote genomic instability and carcinogenesis.

  3. Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation.

    Science.gov (United States)

    Mallik, Saurav; Kundu, Sudip

    2015-01-01

    Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.

  4. Spin-polarized tunneling with GaAs tips in scanning tunneling microscopy

    NARCIS (Netherlands)

    Prins, M.W.J.; Jansen, R.; Kempen, van H.

    1996-01-01

    We describe a model as well as experiments on spin-polarized tunneling with the aid of optical spin orientation. This involves tunnel junctions between a magnetic material and gallium arsenide (GaAs), where the latter is optically excited with circularly polarized light in order to generate

  5. Defining the bacteroides ribosomal binding site.

    Science.gov (United States)

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

    2013-03-01

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

  6. Emergence of robust growth laws from optimal regulation of ribosome synthesis.

    Science.gov (United States)

    Scott, Matthew; Klumpp, Stefan; Mateescu, Eduard M; Hwa, Terence

    2014-08-22

    Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite large-scale changes in protein expression associated with sensing, adaptation, and processing different environmental nutrients, simple growth laws connect the ribosome abundance and the growth rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal regulation that coordinate proteome-wide expression changes with cell growth in a variety of nutrient conditions in the model organism Escherichia coli. We identify supply-driven feedforward activation of ribosomal protein synthesis as the key regulatory motif maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth rate control, irrespective of the details of the molecular implementation. The study highlights the interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental operating constraints, with implications for endogenous and synthetic design of microorganisms. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

  7. Submucosal tunneling techniques: current perspectives.

    Science.gov (United States)

    Kobara, Hideki; Mori, Hirohito; Rafiq, Kazi; Fujihara, Shintaro; Nishiyama, Noriko; Ayaki, Maki; Yachida, Tatsuo; Matsunaga, Tae; Tani, Johji; Miyoshi, Hisaaki; Yoneyama, Hirohito; Morishita, Asahiro; Oryu, Makoto; Iwama, Hisakazu; Masaki, Tsutomu

    2014-01-01

    Advances in endoscopic submucosal dissection include a submucosal tunneling technique, involving the introduction of tunnels into the submucosa. These tunnels permit safer offset entry into the peritoneal cavity for natural orifice transluminal endoscopic surgery. Technical advantages include the visual identification of the layers of the gut, blood vessels, and subepithelial tumors. The creation of a mucosal flap that minimizes air and fluid leakage into the extraluminal cavity can enhance the safety and efficacy of surgery. This submucosal tunneling technique was adapted for esophageal myotomy, culminating in its application to patients with achalasia. This method, known as per oral endoscopic myotomy, has opened up the new discipline of submucosal endoscopic surgery. Other clinical applications of the submucosal tunneling technique include its use in the removal of gastrointestinal subepithelial tumors and endomicroscopy for the diagnosis of functional and motility disorders. This review suggests that the submucosal tunneling technique, involving a mucosal safety flap, can have potential values for future endoscopic developments.

  8. Ultrafast scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Botkin, D.A. [California Univ., Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley Lab., CA (United States)

    1995-09-01

    I have developed an ultrafast scanning tunneling microscope (USTM) based on uniting stroboscopic methods of ultrafast optics and scanned probe microscopy to obtain nanometer spatial resolution and sub-picosecond temporal resolution. USTM increases the achievable time resolution of a STM by more than 6 orders of magnitude; this should enable exploration of mesoscopic and nanometer size systems on time scales corresponding to the period or decay of fundamental excitations. USTM consists of a photoconductive switch with subpicosecond response time in series with the tip of a STM. An optical pulse from a modelocked laser activates the switch to create a gate for the tunneling current, while a second laser pulse on the sample initiates a dynamic process which affects the tunneling current. By sending a large sequence of identical pulse pairs and measuring the average tunnel current as a function of the relative time delay between the pulses in each pair, one can map the time evolution of the surface process. USTM was used to measure the broadband response of the STM`s atomic size tunnel barrier in frequencies from tens to hundreds of GHz. The USTM signal amplitude decays linearly with the tunnel junction conductance, so the spatial resolution of the time-resolved signal is comparable to that of a conventional STM. Geometrical capacitance of the junction does not appear to play an important role in the measurement, but a capacitive effect intimately related to tunneling contributes to the measured signals and may limit the ultimate resolution of the USTM.

  9. The comparison between limited open carpal tunnel release using direct vision and tunneling technique and standard open carpal tunnel release: a randomized controlled trial study.

    Science.gov (United States)

    Suppaphol, Sorasak; Worathanarat, Patarawan; Kawinwongkovit, Viroj; Pittayawutwinit, Preecha

    2012-04-01

    To compare the operative outcome of carpal tunnel release between limited open carpal tunnel release using direct vision and tunneling technique (group A) with standard open carpal tunnel release (group B). Twenty-eight patients were enrolled in the present study. A single blind randomized control trial study was conducted to compare the postoperative results between group A and B. The study parameters were Levine's symptom severity and functional score, grip and pinch strength, and average two-point discrimination. The postoperative results between two groups were comparable with no statistical significance. Only grip strength at three months follow up was significantly greater in group A than in group B. The limited open carpal tunnel release in the present study is effective comparable to the standard open carpal tunnel release. The others advantage of this technique are better cosmesis and improvement in grip strength at the three months postoperative period.

  10. 13th Australian tunnelling conference. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-07-01

    The theme of the conference was 'Engineering in a changing environment'. Topics covered include Australian tunnelling projects, design and development of ground support, tunnelling, international projects, fire and life safety, mining projects, risk management in tunnelling, and tunnel boring machine tunnelling. Papers of particular interest to the coal industry are: improving roadway development in underground coal mine (G. Lewis and G. Gibson), and polymer-based alternative to steel mesh for coal mine strata reinforcement (C. Lukey and others).

  11. Detection of protein-protein interactions by ribosome display and protein in situ immobilisation.

    Science.gov (United States)

    He, Mingyue; Liu, Hong; Turner, Martin; Taussig, Michael J

    2009-12-31

    We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encoding mRNA as ribosome complexes or immobilised on a solid surface. The use of ribosome complexes allows identification of interacting protein partners from their attached coding mRNA. To demonstrate the procedures, we have employed the lymphocyte signalling proteins Vav1 and Grb2 and confirmed the interaction between Grb2 and the N-terminal SH3 domain of Vav1. The method has promise for library screening of pairwise protein interactions, down to the analytical level of individual domain or motif mapping.

  12. Does flexible tunnel drilling affect the femoral tunnel angle measurement after anterior cruciate ligament reconstruction?

    Science.gov (United States)

    Muller, Bart; Hofbauer, Marcus; Atte, Akere; van Dijk, C Niek; Fu, Freddie H

    2015-12-01

    To quantify the mean difference in femoral tunnel angle (FTA) as measured on knee radiographs between rigid and flexible tunnel drilling after anatomic anterior cruciate ligament (ACL) reconstruction. Fifty consecutive patients that underwent primary anatomic ACL reconstruction with a single femoral tunnel drilled with a flexible reamer were included in this study. The control group was comprised of 50 patients all of who underwent primary anatomic ACL reconstruction with a single femoral tunnel drilled with a rigid reamer. All femoral tunnels were drilled through a medial portal to ensure anatomic tunnel placement. The FTA was determined from post-operative anterior-to-posterior (AP) radiographs by two independent observers. A 5° difference between the two mean FTA was considered clinically significant. The average FTA, when drilled with a rigid reamer, was 42.0° ± 7.2°. Drilling with a flexible reamer resulted in a mean FTA of 44.7° ± 7.0°. The mean difference of 2.7° was not statistically significant. The intraclass correlation coefficient for inter-tester reliability was 0.895. The FTA can be reliably determined from post-operative AP radiographs and provides a useful and reproducible metric for characterizing femoral tunnel position after both rigid and flexible femoral tunnel drilling. This has implications for post-operative evaluation and preoperative treatment planning for ACL revision surgery. IV.

  13. Derivation of the tunnelling exchange time for the model of trap-assisted tunnelling

    International Nuclear Information System (INIS)

    Racko, J.; Ballo, P.; Benko, P.; Harmatha, L.; Grmanova, A.; Breza, J.

    2014-01-01

    We present derivation of the tunnelling exchange times that play the key role in the model of trap assisted tunnelling (TAT) considering the electron and hole exchange processes between the trapping centre lying in the forbidden band of the semiconductor and the conduction band, valence band or a metal. All exchange processes are quantitatively described by respective exchange times. The reciprocal values of these exchange times represent the frequency with which the exchange processes contribute to the probability of occupation of the trap by free charge carriers. The crucial problem in any model of TAT is the calculation of the occupation probability. In our approach this probability is expressed in terms of only thermal and tunnelling exchange times. The concept of tunnelling exchange times presents a dominant contribution to our model of TAT. The new approach allows to simply calculate the probability of occupation of the trapping centre by a free charge carrier and subsequently to get the thermal and tunnelling generation-recombination rates occurring in the continuity equations. This is why the TAT model based on thermal and tunnelling exchange times is suitable for simulating the electrical properties of semiconductor nanostructures in which quantum mechanical phenomena play a key role. (authors)

  14. Electronic noise of superconducting tunnel junction detectors

    International Nuclear Information System (INIS)

    Jochum, J.; Kraus, H.; Gutsche, M.; Kemmather, B.; Feilitzsch, F. v.; Moessbauer, R.L.

    1994-01-01

    The optimal signal to noise ratio for detectors based on superconducting tunnel junctions is calculated and compared for the cases of a detector consisting of one single tunnel junction, as well as of series and of parallel connections of such tunnel junctions. The influence of 1 / f noise and its dependence on the dynamical resistance of tunnel junctions is discussed quantitatively. A single tunnel junction yields the minimum equivalent noise charge. Such a tunnel junction exhibits the best signal to noise ratio if the signal charge is independent of detector size. In case, signal charge increases with detector size, a parallel or a series connection of tunnel junctions would provide the optimum signal to noise ratio. The equivalent noise charge and the respective signal to noise ratio are deduced as functions of tunnel junction parameters such as tunneling time, quasiparticle lifetime, etc. (orig.)

  15. The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes

    Directory of Open Access Journals (Sweden)

    Mickey R. Miller

    2014-09-01

    Full Text Available In bacteria, transfer-messenger RNA (tmRNA and SmpB comprise the most common and effective system for rescuing stalled ribosomes. Ribosomes stall on mRNA transcripts lacking stop codons and are rescued as the defective mRNA is swapped for the tmRNA template in a process known as trans-translation. The tmRNA–SmpB complex is recruited to the ribosome independent of a codon–anticodon interaction. Given that the ribosome uses robust discriminatory mechanisms to select against non-cognate tRNAs during canonical decoding, it has been hard to explain how this can happen. Recent structural and biochemical studies show that SmpB licenses tmRNA entry through its interactions with the decoding center and mRNA channel. In particular, the C-terminal tail of SmpB promotes both EFTu activation and accommodation of tmRNA, the former through interactions with 16S rRNA nucleotide G530 and the latter through interactions with the mRNA channel downstream of the A site. Here we present a detailed model of the earliest steps in trans-translation, and in light of these mechanistic considerations, revisit the question of how tmRNA preferentially reacts with stalled, non-translating ribosomes.

  16. Tunneling of Atoms, Nuclei and Molecules

    International Nuclear Information System (INIS)

    Bertulani, C.A.

    2015-01-01

    This is a brief review of few relevant topics on tunneling of composite particles and how the coupling to intrinsic and external degrees of freedom affects tunneling probabilities. I discuss the phenomena of resonant tunneling, different barriers seen by subsystems, damping of resonant tunneling by level bunching and continuum effects due to particle dissociation. (author)

  17. 45 CFR 670.34 - Entry and exit ports.

    Science.gov (United States)

    2010-10-01

    ... ANTARCTIC ANIMALS AND PLANTS Import Into and Export From the United States § 670.34 Entry and exit ports. (a) Any native mammal, native bird, or native plants taken within Antarctica that are imported into or... Orleans, Louisiana. (7) New York, New York. (8) Seattle, Washington. (9) Dallas/Fort Worth, Texas. (10...

  18. Chaos regularization of quantum tunneling rates

    International Nuclear Information System (INIS)

    Pecora, Louis M.; Wu Dongho; Lee, Hoshik; Antonsen, Thomas; Lee, Ming-Jer; Ott, Edward

    2011-01-01

    Quantum tunneling rates through a barrier separating two-dimensional, symmetric, double-well potentials are shown to depend on the classical dynamics of the billiard trajectories in each well and, hence, on the shape of the wells. For shapes that lead to regular (integrable) classical dynamics the tunneling rates fluctuate greatly with eigenenergies of the states sometimes by over two orders of magnitude. Contrarily, shapes that lead to completely chaotic trajectories lead to tunneling rates whose fluctuations are greatly reduced, a phenomenon we call regularization of tunneling rates. We show that a random-plane-wave theory of tunneling accounts for the mean tunneling rates and the small fluctuation variances for the chaotic systems.

  19. Excavation of the Surikamigawa dam diversion tunnel. Surikamigawa dam karihaisui tunnel kantsu

    Energy Technology Data Exchange (ETDEWEB)

    Ikeda, T.; Konno, T. (Ministry of Construction, Tokyo (Japan))

    1994-04-01

    A bypass tunnel construction has been completed at the Surikamigawa dam (Japan). This paper describes the summary of the construction. The full-swing dam construction work is scheduled to begin in 1995. The soils distributed near the dam site consist of lapillus tuff containing andesite-based light stones and tuff-based conglomerates containing large gravels. Excavation of the dam diversion tunnel has used a blasting method, and the tunnel construction has adopted an automatic tunnel cross section marking system and a non-electric explosion method. This marking system is a system to irradiate a laser beam onto the facing to depict excavation lines that realizes labor saving and high-accuracy excavation. The error at the tunnel completion was found 20 mm. The non-electric explosion method ignites a coated explosive layer with an impact wave, which is electrostatically safe, and reduces blasting vibration. Electric detonators have also been used because of using ANFO explosives. The result obtained from measurements of inner space displacement necessary for the blasting process has indicated that the area near the dam site consists of stable mountains. 6 figs., 4 tabs.

  20. Charge Islands Through Tunneling

    Science.gov (United States)

    Robinson, Daryl C.

    2002-01-01

    It has been recently reported that the electrical charge in a semiconductive carbon nanotube is not evenly distributed, but rather it is divided into charge "islands." This paper links the aforementioned phenomenon to tunneling and provides further insight into the higher rate of tunneling processes, which makes tunneling devices attractive. This paper also provides a basis for calculating the charge profile over the length of the tube so that nanoscale devices' conductive properties may be fully exploited.

  1. Tunneling progress on the Yucca Mountain Project

    International Nuclear Information System (INIS)

    Hansmire, W.H.; Munzer, R.J.

    1996-01-01

    The current status of tunneling progress on the Yucca Mountain Project (YMP) is presented in this paper. The Exploratory Studies Facility (ESF), a key part of the YMP, has been long in development and construction is ongoing. This is a progress report on the tunneling aspects of the ESF as of January 1, 1996. For purposes of discussion in this summary, the tunneling has progressed in four general phases. The paper describes: tunneling in jointed rock under low stress; tunneling through the Bow Ridge Fault and soft rock; tunneling through the Imbricate Fault Zone; and Tunneling into the candidate repository formation

  2. Road vehicle emissions of molecular hydrogen (H 2) from a tunnel study

    Science.gov (United States)

    Vollmer, Martin K.; Juergens, Niklas; Steinbacher, Martin; Reimann, Stefan; Weilenmann, Martin; Buchmann, Brigitte

    Motor vehicle combustion emissions of molecular hydrogen (H 2), carbon monoxide (CO), and carbon dioxide (CO 2) were measured during a 6-week period from November 2004 to January 2005 in Gubrist Tunnel, Switzerland, to determine vehicle emission factors for these trace gases and the ratios of the concentration growths ΔH2/ΔCO and ΔH2/ΔCO2 in the tunnel under real-world highway driving conditions. For H 2, molar mixing ratios at the tunnel exit were found to be 7-10 ppm (parts-per-million, 10-6) during rush hours. Mean emission factors of E=49.7(±16.5)mgkm-1, ECO=1.46(±0.54)gkm-1, and E=266(±69)gkm-1 were calculated. E was largest during weekday rush-hour traffic, a consequence of the more frequent accelerations in congested traffic when fuel combustion is not optimal. E was smaller for heavy-duty vehicles (HDV) compared to light-duty vehicles (LDV), a finding which was attributed to the diesel vs. gasoline engine technology. The mean ΔH2/ΔCO molecular ratio was 0.48±0.12. This ratio increased to ˜0.6 during rush hours, suggesting that H 2 yield is favored relative to CO under fuel-rich conditions, presumably a consequence of an increasing contribution of the water-gas-shift reaction. The mean ΔH2/ΔCO2 molecular ratio was 4.4×10-3 but reduced to 2.5×10-3 when the relative HDV abundance was at maximum. Using three different approaches, road traffic H 2 emissions were estimated for 2004 for Switzerland at 5.0-6.6 Gg and globally at 4.2-8.1 Tg. Despite projections of increasing traffic, Swiss H 2 emissions are not expected to change significantly in the near future, and global emissions are likely to decrease due to improved exhaust gas clean-up technologies.

  3. Peak stresses shift from femoral tunnel aperture to tibial tunnel aperture in lateral tibial tunnel ACL reconstructions: a 3D graft-bending angle measurement and finite-element analysis.

    Science.gov (United States)

    Van Der Bracht, Hans; Tampere, Thomas; Beekman, Pieter; Schepens, Alexander; Devriendt, Wouter; Verdonk, Peter; Victor, Jan

    2018-02-01

    To investigate the effect of tibial tunnel orientation on graft-bending angle and stress distribution in the ACL graft. Eight cadaveric knees were scanned in extension, 45°, 90°, and full flexion. 3D reconstructions with anatomically placed anterior cruciate ligament (ACL) grafts were constructed with Mimics 14.12 ® . 3D graft-bending angles were measured for classic medial tibial tunnels (MTT) and lateral tibial tunnels (LTT) with different drill-guide angles (DGA) (45°, 55°, 65°, and 75°). A pivot shift was performed on 1 knee in a finite-element analysis. The peak stresses in the graft were calculated for eight different tibial tunnel orientations. In a classic anatomical ACL repair, the largest graft-bending angle and peak stresses are seen at the femoral tunnel aperture. The use of a different DGA at the tibial side does not change the graft-bending angle at the femoral side or magnitude of peak stresses significantly. When using LTT, the largest graft-bending angles and peak stresses are seen at the tibial tunnel aperture. In a classic anatomical ACL repair, peak stresses in the ACL graft are found at the femoral tunnel aperture. When an LTT is used, peak stresses are similar compared to classic ACL repairs, but the location of the peak stress will shift from the femoral tunnel aperture towards the tibial tunnel aperture. the risk of graft rupture is similar for both MTTs and LTTs, but the location of graft rupture changes from the femoral tunnel aperture towards the tibial tunnel aperture, respectively. I.

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

    Science.gov (United States)

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

    2015-06-01

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

  5. Hypersonic Tunnel Facility (HTF)

    Data.gov (United States)

    Federal Laboratory Consortium — The Hypersonic Tunnel Facility (HTF) is a blow-down, non-vitiated (clean air) free-jet wind tunnel capable of testing large-scale, propulsion systems at Mach 5, 6,...

  6. Klein tunneling phenomenon with pair creation process

    Science.gov (United States)

    Wu, G. Z.; Zhou, C. T.; Fu, L. B.

    2018-01-01

    In this paper, we study the Klein tunneling phenomenon with electron-positron pair creation process. Pairs can be created from the vacuum by a supercritical single-well potential (for electrons). In the time region, the time-dependent growth pattern of the created pairs can be characterized by four distinct regimes which can be considered as four different statuses of the single well. We find that if positrons penetrate the single well by Klein tunneling in different statuses, the total number of the tunneling positrons will be different. If Klein tunneling begins at the initial stage of the first status i.e. when the sing well is empty, the tunneling process and the total number of tunneling positrons are similar to the traditional Klein tunneling case without considering the pair creation process. As the tunneling begins later, the total tunneling positron number increases. The number will finally settle to an asymptotic value when the tunneling begins later than the settling-down time t s of the single well which has been defined in this paper.

  7. [Identification of Clonorchis sinensis metacercariae based on PCR targeting ribosomal DNA ITS regions and COX1 gene].

    Science.gov (United States)

    Yang, Qing-Li; Shen, Ji-Qing; Jiang, Zhi-Hua; Yang, Yi-Chao; Li, Hong-Mei; Chen, Ying-Dan; Zhou, Xiao-Nong

    2014-06-01

    To identify Clonorchis sinensis metacercariae using PCR targeting ribosomal DNA ITS region and COX1 gene. Pseudorasbora parva were collected from Hengxian County of Guangxi at the end of May 2013. Single metacercaria of C. sinensis and other trematodes were separated from muscle tissue of P. parva by digestion method. Primers targeting ribosomal DNA ITS region and COX1 gene of C. sinensis were designed for PCR and the universal primers were used as control. The sensitivity and specificity of the PCR detection were analyzed. C. sinensis metacercariae at different stages were identified by PCR. DNA from single C. sinensis metacercaria was detected by PCR targeting ribosomal DNA ITS region and COX1 gene. The specific amplicans have sizes of 437/549, 156/249 and 195/166 bp, respectively. The ratio of the two positive numbers in PCR with universal primers and specific primers targeting C. sinensis ribosomal DNA ITS1 and ITS2 regions was 0.905 and 0.952, respectively. The target gene fragments were amplified by PCR using COX1 gene-specific primers. The PCR with specific primers did not show any non-specific amplification. However, the PCR with universal primers targeting ribosomal DNA ITS regions performed serious non-specific amplification. C. sinensis metacercariae at different stages are identified by morphological observation and PCR method. Species-specific primers targeting ribosomal DNA ITS region show higher sensitivity and specificity than the universal primers. PCR targeting COX1 gene shows similar sensitivity and specificity to PCR with specific primers targeting ribosomal DNA ITS regions.

  8. Tunneling time, what is its meaning?

    International Nuclear Information System (INIS)

    McDonald, C R; Orlando, G; Vampa, G; Brabec, T

    2015-01-01

    The tunnel time ionization dynamics for bound systems in laser fields are investigated. Numerical analysis for a step function switch-on of the field allows for the tunnel time to be defined as the time it takes the ground state to develop the under-barrier wavefunction components necessary to achieve the static field ionization rate. A relation between the tunnel time and the Keldysh time is established. The definition of the tunnel time is extended to time varying fields and experimental possibilities for measuring the tunnel time are discussed

  9. Transonic Dynamics Tunnel (TDT)

    Data.gov (United States)

    Federal Laboratory Consortium — The Transonic Dynamics Tunnel (TDT) is a continuous flow wind-tunnel facility capable of speeds up to Mach 1.2 at stagnation pressures up to one atmosphere. The TDT...

  10. A simplified approach for exit dose in vivo measurements in radiotherapy and its clinical application

    International Nuclear Information System (INIS)

    Banjade, D.P.; Shukri, A.; Tajuddin, A.A.; Shrestha, S.L.; Bhat, M.

    2002-01-01

    This is a study using LiF:Mg;Ti thermoluminescent dosimeter (TLD) rods in phantoms to investigate the effect of lack of backscatter on exit dose. Comparing the measured dose with anticipated dose calculated using tissue maximum ratio (TMR) or percentage depth dose (PDD) gives rise to a correction factor. This correction factor may be applied to in-vivo dosimetry results to derive true dose to a point within the patient. Measurements in a specially designed humanoid breast phantom as well as patients undergoing radiotherapy treatment were also been done. TLDs with reproducibility of within ±3% (1 SD) are irradiated in a series of measurements for 6 and 10 MV photon beams from a medical linear accelerator. The measured exit doses for the different phantom thickness for 6 MV beams are found to be lowered by 10.9 to 14.0% compared to the dose derived from theoretical estimation (normalized dose at d max ). The same measurements for 10 MV beams are lowered by 9.0 to 13.5%. The variations of measured exit dose for different field sizes are found to be within 2.5%. The exit doses with added backscatter material from 2 mm up to 15 cm, shows gradual increase and the saturated values agreed within 1.5% with the expected results for both beams. The measured exit doses in humanoid breast phantom as well as in the clinical trial on patients undergoing radiotherapy also agreed with the predicted results based on phantom measurements. The authors' viewpoint is that this technique provides sufficient information to design exit surface bolus to restore build down effect in cases where part of the exit surface is being considered as a target volume. It indicates that the technique could be translated for in vivo dose measurements, which may be a conspicuous step of quality assurance in clinical practice. Copyright (2002) Australasian College of Physical Scientists and Engineers in Medicine

  11. Effects of neglecting carrier tunneling on electrostatic potential in calculating direct tunneling gate current in deep submicron MOSFETs

    OpenAIRE

    Hakim, MMA; Haque, A

    2002-01-01

    We investigate the validity of the assumption of neglecting carrier tunneling effects on self-consistent electrostatic potential in calculating direct tunneling gate current in deep submicron MOSFETs. Comparison between simulated and experimental results shows that for accurate modeling of direct tunneling current, tunneling effects on potential profile need to be considered. The relative error in gate current due to neglecting carrier tunneling is higher at higher gate voltages and increases...

  12. Association of rheumatic diseases with early exit from paid employment in Portugal.

    Science.gov (United States)

    Laires, Pedro A; Gouveia, Miguel

    2014-04-01

    To examine the association between rheumatic diseases (RD) and other chronic morbidity with early exit from paid employment in the Portuguese population. The study population consisted of all people between 50 and 64 years of age (3,762 men and 4,241 women) who participated in the Portuguese National Health Survey, conducted in 2005/2006. Data were collected on demographics, ill-health, lifestyle, and socioeconomic factors. Logistic regression was used to estimate the isolated effect of rheumatic diseases and other chronic diseases on the likelihood of exit from paid employment. At the time of the survey, 45.1 % of the Portuguese population with ages between 50 and 64 years old were not employed. In the nonemployed population, 31.6 % self-reported "poor" to "very poor" health, whereas 16.4 % did so in the employed population. A larger average number of major chronic diseases per capita were also found in those not employed (1.9 vs. 1.4, p paid employment. In particular, rheumatic diseases were more prevalent (43.4 vs. 32.1 %) and associated with early exit from work (OR 1.31; CI 1.12-1.52, p = 0.001). This study suggests an association between RD and other major chronic diseases with early exit from paid employment in Portugal. Thus, health and social protection policies should target these chronic disorders in order to better address sustainability issues and social protection effectiveness.

  13. Airport exit and entry screening for Ebola--August-November 10, 2014.

    Science.gov (United States)

    Brown, Clive M; Aranas, Aaron E; Benenson, Gabrielle A; Brunette, Gary; Cetron, Marty; Chen, Tai-Ho; Cohen, Nicole J; Diaz, Pam; Haber, Yonat; Hale, Christa R; Holton, Kelly; Kohl, Katrin; Le, Amanda W; Palumbo, Gabriel J; Pearson, Kate; Phares, Christina R; Alvarado-Ramy, Francisco; Roohi, Shah; Rotz, Lisa D; Tappero, Jordan; Washburn, Faith M; Watkins, James; Pesik, Nicki

    2014-12-12

    In response to the largest recognized Ebola virus disease epidemic now occurring in West Africa, the governments of affected countries, CDC, the World Health Organization (WHO), and other international organizations have collaborated to implement strategies to control spread of the virus. One strategy recommended by WHO calls for countries with Ebola transmission to screen all persons exiting the country for "unexplained febrile illness consistent with potential Ebola infection." Exit screening at points of departure is intended to reduce the likelihood of international spread of the virus. To initiate this strategy, CDC, WHO, and other global partners were invited by the ministries of health of Guinea, Liberia, and Sierra Leone to assist them in developing and implementing exit screening procedures. Since the program began in August 2014, an estimated 80,000 travelers, of whom approximately 12,000 were en route to the United States, have departed by air from the three countries with Ebola transmission. Procedures were implemented to deny boarding to ill travelers and persons who reported a high risk for exposure to Ebola; no international air traveler from these countries has been reported as symptomatic with Ebola during travel since these procedures were implemented.

  14. Toward electron exit wave tomography of amorphous materials at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Borisenko, Konstantin B., E-mail: konstantin.borisenko@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Moldovan, Grigore [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Kirkland, Angus I., E-mail: angus.kirkland@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Van Dyck, Dirk [Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Tang, Hsin-Yu; Chen, Fu-Rong [Department of Engineering and System Science, National Tsing Hua University, Kuang-Fu Road, 300 Hsinchu, Taiwan (China)

    2012-09-25

    Highlights: Black-Right-Pointing-Pointer We suggest a novel electron exit wave tomography approach to obtain three dimensional atomic structures of amorphous materials. Black-Right-Pointing-Pointer Theoretical tests using a model of amorphous Si doped with Au show that it is feasible to reconstruct both Si and Au atoms positions. Black-Right-Pointing-Pointer Reconstructions of the strongly scattering Au atoms positions appear to be insensitive to typical experimental errors. - Abstract: We suggest to use electron exit wave phase for tomographic reconstruction of structure of Au-doped amorphous Si with atomic resolution. In the present theoretical investigation into the approach it is found that the number of projections and the accuracy of defocus in the focal series restoration are the main factors that contribute to the final resolution. Although resolution is ultimately limited by these factors, phase shifts in the exit wave are sufficient to identify the position of Au atoms in an amorphous Si needle model, even when only 19 projections with defocus error of 4 nm are used. Electron beam damage will probably further limit the resolution of such tomographic reconstructions, however beam damage can be mitigated using lower accelerating voltages.

  15. A balance of FGF and BMP signals regulates cell cycle exit and Equarin expression in lens cells

    Science.gov (United States)

    Jarrin, Miguel; Pandit, Tanushree; Gunhaga, Lena

    2012-01-01

    In embryonic and adult lenses, a balance of cell proliferation, cell cycle exit, and differentiation is necessary to maintain physical function. The molecular mechanisms regulating the transition of proliferating lens epithelial cells to differentiated primary lens fiber cells are poorly characterized. To investigate this question, we used gain- and loss-of-function analyses to modulate fibroblast growth factor (FGF) and/or bone morphogenetic protein (BMP) signals in chick lens/retina explants. Here we show that FGF activity plays a key role for proliferation independent of BMP signals. Moreover, a balance of FGF and BMP signals regulates cell cycle exit and the expression of Ccdc80 (also called Equarin), which is expressed at sites where differentiation of lens fiber cells occurs. BMP activity promotes cell cycle exit and induces Equarin expression in an FGF-dependent manner. In contrast, FGF activity is required but not sufficient to induce cell cycle exit or Equarin expression. Furthermore, our results show that in the absence of BMP activity, lens cells have increased cell cycle length or are arrested in the cell cycle, which leads to decreased cell cycle exit. Taken together, these findings suggest that proliferation, cell cycle exit, and early differentiation of primary lens fiber cells are regulated by counterbalancing BMP and FGF signals. PMID:22718906

  16. Road and Railroad Tunnels

    Data.gov (United States)

    Department of Homeland Security — Tunnels in the United States According to the HSIP Tiger Team Report, a tunnel is defined as a linear underground passageway open at both ends. This dataset is based...

  17. Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells.

    Science.gov (United States)

    Tan, Thomas C J; Knight, John; Sbarrato, Thomas; Dudek, Kate; Willis, Anne E; Zamoyska, Rose

    2017-07-25

    Global transcriptomic and proteomic analyses of T cells have been rich sources of unbiased data for understanding T-cell activation. Lack of full concordance of these datasets has illustrated that important facets of T-cell activation are controlled at the level of translation. We undertook translatome analysis of CD8 T-cell activation, combining polysome profiling and microarray analysis. We revealed that altering T-cell receptor stimulation influenced recruitment of mRNAs to heavy polysomes and translation of subsets of genes. A major pathway that was compromised, when TCR signaling was suboptimal, was linked to ribosome biogenesis, a rate-limiting factor in both cell growth and proliferation. Defective TCR signaling affected transcription and processing of ribosomal RNA precursors, as well as the translation of specific ribosomal proteins and translation factors. Mechanistically, IL-2 production was compromised in weakly stimulated T cells, affecting the abundance of Myc protein, a known regulator of ribosome biogenesis. Consequently, weakly activated T cells showed impaired production of ribosomes and a failure to maintain proliferative capacity after stimulation. We demonstrate that primary T cells respond to various environmental cues by regulating ribosome biogenesis and mRNA translation at multiple levels to sustain proliferation and differentiation.

  18. PUREX Storage Tunnels dangerous waste permit application

    International Nuclear Information System (INIS)

    1991-12-01

    The PUREX Storage Tunnels are a mixed waste storage unit consisting of two underground railroad tunnels: Tunnel Number 1 designated 218-E-14 and Tunnel Number 2 designated 218-E-15. The two tunnels are connected by rail to the PUREX Plant and combine to provide storage space for 48 railroad cars (railcars). The PUREX Storage Tunnels provide a long-term storage location for equipment removed from the PUREX Plant. Transfers into the PUREX Storage Tunnels are made on an as-needed basis. Radioactively contaminated equipment is loaded on railcars and remotely transferred by rail into the PUREX Storage Tunnels. Railcars act as both a transport means and a storage platform for equipment placed into the tunnels. This report consists of part A and part B. Part A reports on amounts and locations of the mixed water. Part B permit application consists of the following: Facility Description and General Provisions; Waste Characteristics; Process Information; Groundwater Monitoring; Procedures to Prevent Hazards; Contingency Plan; Personnel Training; Exposure Information Report

  19. (Brassicaceae) based on nuclear ribosomal ITS DNA sequences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 2. Phylogeny and biogeography of Alyssum (Brassicaceae) based on nuclear ribosomal ITS DNA sequences. Yan Li Yan Kong Zhe Zhang Yanqiang Yin Bin Liu Guanghui Lv Xiyong Wang. Research Article Volume 93 Issue 2 August 2014 pp 313-323 ...

  20. Architecture of the E.coli 70S ribosome

    DEFF Research Database (Denmark)

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

    1997-01-01

    The 70S ribosome from E.coli was analysed by neutron scattering focusing on the shape and the internal protein-RNA-distribution of the complex. Measurements on selectively deuterated 70S particles and free 30S and 50S subunits applying conventional contrast variation and proton-spin contrast...