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

PubMed Central

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

2014-01-01

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2Ile) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2Ile binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes. PMID:24344322

tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

PubMed Central

Marck, Christian; Grosjean, Henri

2002-01-01

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria. PMID:12403461

Structural insights into translational recoding by frameshift suppressor tRNA SufJ

DOE PAGES

Fagan, Crystal E.; Maehigashi, Tatsuya; Dunkle, Jack A.; ...

2014-10-28

The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA SufJ, a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA SufJ contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL SufJ ormore » tRNA SufJ does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL SufJ and ASL Thr bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34–37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL SufJ imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA SufJ during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.« less

Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A.

PubMed

Stuart, J W; Gdaniec, Z; Guenther, R; Marszalek, M; Sochacka, E; Malkiewicz, A; Agris, P F

2000-11-07

The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding.

Ribosome hijacking: a role for small protein B during trans-translation

PubMed Central

Nonin-Lecomte, Sylvie; Germain-Amiot, Noella; Gillet, Reynald; Hallier, Marc; Ponchon, Luc; Dardel, Frédéric; Felden, Brice

2009-01-01

Tight recognition of codon–anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the ‘tmRNA–SmpB' system (transfer messenger RNA–small protein B). Remarkably, entry and accommodation of aminoacylated-tmRNA into stalled ribosomes occur without a codon–anticodon interaction but in the presence of SmpB. Here, we show that within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon–anticodon pairing occurs. The footprints at positions A1492 and A1493 of a small decoding centre, as well as on a set of conserved SmpB amino acids, were identified by nuclear magnetic resonance. Mutants at these residues display the same growth defects as for ΔsmpB strains. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon. PMID:19132006

Ribosome hijacking: a role for small protein B during trans-translation.

PubMed

Nonin-Lecomte, Sylvie; Germain-Amiot, Noella; Gillet, Reynald; Hallier, Marc; Ponchon, Luc; Dardel, Frédéric; Felden, Brice

2009-02-01

Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). Remarkably, entry and accommodation of aminoacylated-tmRNA into stalled ribosomes occur without a codon-anticodon interaction but in the presence of SmpB. Here, we show that within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs. The footprints at positions A1492 and A1493 of a small decoding centre, as well as on a set of conserved SmpB amino acids, were identified by nuclear magnetic resonance. Mutants at these residues display the same growth defects as for DeltasmpB strains. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon.

Energetics of codon-anticodon recognition on the small ribosomal subunit.

PubMed

Almlöf, Martin; Andér, Martin; Aqvist, Johan

2007-01-09

Recent crystal structures of the small ribosomal subunit have made it possible to examine the detailed energetics of codon recognition on the ribosome by computational methods. The binding of cognate and near-cognate anticodon stem loops to the ribosome decoding center, with mRNA containing the Phe UUU and UUC codons, are analyzed here using explicit solvent molecular dynamics simulations together with the linear interaction energy (LIE) method. The calculated binding free energies are in excellent agreement with experimental binding constants and reproduce the relative effects of mismatches in the first and second codon position versus a mismatch at the wobble position. The simulations further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with the Phe UUU codon. It is also found that the ribosome significantly enhances the intrinsic stability differences of codon-anticodon complexes in aqueous solution. Structural analysis of the simulations confirms the previously suggested importance of the universally conserved nucleotides A1492, A1493, and G530 in the decoding process.

On origin of genetic code and tRNA before translation

PubMed Central

2011-01-01

Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule. Conclusion Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony. Reviewers This article was reviewed by Eugene V. Koonin, Wentao Ma (nominated by Juergen Brosius) and Anthony Poole. PMID:21342520

The presence of codon-anticodon pairs in the acceptor stem of tRNAs.

PubMed Central

Rodin, S; Rodin, A; Ohno, S

1996-01-01

A total of 1268 available (excluding mitochondrial) tRNA sequences was used to reconstruct the common consensus image of their acceptor domains. Its structure appeared as a 11-bp-long double-stranded palindrome with complementary triplets in the center, each flanked by the 3'-ACCD and NGGU-5' motifs on each strand (D, base determinator). The palindrome readily extends up to the modern tRNA-like cloverleaf passing through an intermediate hairpin having in the center the single-stranded triplet, in supplement to its double-stranded precursor. The latter might represent an original anticodon-codon pair mapped at 1-2-3 positions of the present-day tRNA acceptors. This conclusion is supported by the striking correlation: in pairs of consensus tRNAs with complementary anticodons, their bases at the 2nd position of the acceptor stem were also complementary. Accordingly, inverse complementarity was also evident at the 71st position of the acceptor stem. With a single exception (tRNA(Phe)-tRNA(Glu) pair), the parallelism is especially impressive for the pairs of tRNAs recognized by aminoacyl-tRNA synthetases (aaRS) from the opposite classes. The above complementarity still doubly presented at the key central position of real single-stranded anticodons and their hypothetical double-stranded precursors is consistent with our previous data pointing to the double-strand use of ancient RNAs in the origin of the main actors in translation- tRNAs with complementary anticodons and the two classes of aaRS. Images Fig. 3 Table 2 Fig. 4 PMID:8643439

Evolution of E. coli tRNA(Trp)

NASA Technical Reports Server (NTRS)

Staves, Mark P.; Lacey, James C., Jr.; Bloch, David P.

1988-01-01

It has been shown by Lacey et al. (1985) that, in general, the hydrophobicity ranking of an amino acid correlates with that of its anticodonic nucleotide, with tryptophan being one of the four amino acids for which this rule does not apply. It was proposed that this failure to correlate was due to the fact that the anticodon assignments for the four amino acids were made late, after the mutation of existing tRNAs. In this paper, the evolution of E. coli tRNA(Trp) is examined by comparing its homology with other E. coli tRNAs. The results demonstrate the presence of an evolutionary relationship between E. coli tRNA(Trp) and tRNA(Gly) or tRNA(Arg) molecules, and support the idea of the late assignment of anticodon to Trp.

The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS.

PubMed Central

Rudinger-Thirion, J; Giegé, R

1999-01-01

The wild-type transcript of Escherichia coli tRNASec, characterized by a peculiar core architecture and a large variable region, was shown to be aspartylatable by yeast AspRS. Similar activities were found for tRNASec mutants with methionine, leucine, and tryptophan anticodons. The charging efficiency of these molecules was found comparable to that of a minihelix derived from tRNAAsp and is accounted for by the presence of the discriminator residue G73, which is a major aspartate identity determinant. Introducing the aspartate identity elements from the anticodon loop (G34, U35, C36, C38) into tRNASec transforms this molecule into an aspartate acceptor with kinetic properties identical to tRNAAsp. Expression of the aspartate identity set in tRNASec is independent of the size of its variable region. The functional study was completed by footprinting experiments with four different nucleases as structural probes. Protection patterns by AspRS of transplanted tRNASec and tRNAAsp were found similar. They are modified, particularly in the anticodon loop, upon changing the aspartate anticodon into that of methionine. Altogether, it appears that recognition of a tRNA by AspRS is more governed by the presence of the aspartate identity set than by the structural framework that carries this set. PMID:10199566

Insights into factorless translational initiation by the tRNA-like pseudoknot domain of a viral IRES.

PubMed

Au, Hilda H T; Jan, Eric

2012-01-01

The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors. The pseudoknot I (PKI) domain of the IRES mimics a tRNA-like codon:anticodon interaction in the ribosomal P site to direct translation initiation from a non-AUG initiation codon in the A site. In this study, we have performed a comprehensive mutational analysis of this region to delineate the molecular parameters that drive IRES translation. We demonstrate that IRES-mediated translation can initiate at an alternate adjacent and overlapping start site, provided that basepairing interactions within PKI remain intact. Consistent with this, IGR IRES translation tolerates increases in the variable loop region that connects the anticodon- and codon-like elements within the PKI domain, as IRES activity remains relatively robust up to a 4-nucleotide insertion in this region. Finally, elements from an authentic tRNA anticodon stem-loop can functionally supplant corresponding regions within PKI. These results verify the importance of the codon:anticodon interaction of the PKI domain and further define the specific elements within the tRNA-like domain that contribute to optimal initiator Met-tRNA(i)-independent IRES translation.

Insights into Factorless Translational Initiation by the tRNA-Like Pseudoknot Domain of a Viral IRES

PubMed Central

Au, Hilda H. T.; Jan, Eric

2012-01-01

The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors. The pseudoknot I (PKI) domain of the IRES mimics a tRNA-like codon:anticodon interaction in the ribosomal P site to direct translation initiation from a non-AUG initiation codon in the A site. In this study, we have performed a comprehensive mutational analysis of this region to delineate the molecular parameters that drive IRES translation. We demonstrate that IRES-mediated translation can initiate at an alternate adjacent and overlapping start site, provided that basepairing interactions within PKI remain intact. Consistent with this, IGR IRES translation tolerates increases in the variable loop region that connects the anticodon- and codon-like elements within the PKI domain, as IRES activity remains relatively robust up to a 4-nucleotide insertion in this region. Finally, elements from an authentic tRNA anticodon stem-loop can functionally supplant corresponding regions within PKI. These results verify the importance of the codon:anticodon interaction of the PKI domain and further define the specific elements within the tRNA-like domain that contribute to optimal initiator Met-tRNAi-independent IRES translation. PMID:23236506

Possibilities for the evolution of the genetic code from a preceding form

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1973-01-01

Analysis of the interaction between mRNA codons and tRNA anticodons suggests a model for the evolution of the genetic code. Modification of the nucleic acid following the anticodon is at present essential in both eukaryotes and prokaryotes to ensure fidelity of translation of codons starting with A, and the amino acids which could be coded for before the evolution of the modifying enzymes can be deduced.

The role of modifications in codon discrimination by tRNA(Lys)UUU.

PubMed

Murphy, Frank V; Ramakrishnan, Venki; Malkiewicz, Andrzej; Agris, Paul F

2004-12-01

The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t(6)A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm(5)U34 or s(2)U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.

Summary of evidence for an anticodonic basis for the origin of the genetic code

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1981-01-01

This article summarizes data supporting the hypothesis that the genetic code origin was based on relationships (probably affinities) between amino acids and their anticodon nucleotides. Selective activation seems to follow from selective affinity and consequently, incorporation of amino acids into peptides can also be selective. It is suggested that these selectivities in affinity and activation, coupled with the base pairing specificities, allowed the origin of the code and the process of translation.

A theoretical thermochemical study of solute-solvent dielectric effects in the displacement of codon-anticodon base pairs

NASA Astrophysics Data System (ADS)

Monajjemi, M.; Razavian, M. H.; Mollaamin, F.; Naderi, F.; Honarparvar, B.

2008-12-01

Quantum-chemical solvent effect theories describe the electronic structure of a molecular subsystem embedded in a solvent or other molecular environment. The solvation of biomolecules is important in molecular biology, since numerous processes involve proteins interacting in changing solvent-solute systems. In this theoretical study, we focus on mRNA-tRNA base pairs as a fundamental step in protein synthesis influenced by hydrogen bonding between two antiparallel trinucleotides, namely, the mRNA codon and tRNA anticodon. We use the mean reaction field theories, which describe electrostatic and polarization interactions between solute and solvent in the AAA, UUU, AAG, and UUC triplex sequences optimized in various solvent media such as water, dimethylsulfoxide, methanol, ethanol, and cyclopean using the self-consistent reaction field model. This process depends on either the reaction potential function of the solvent or charge transfer operators that appear in solute-solvent interaction. Because of codon and anticodon biological criteria, we performed nonempirical quantum-mechanical calculations at the BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and five solvents at three temperatures. Finally, to obtain more information, we calculated thermochemical parameters to find that the dielectric constant of solvents plays an important role in the displacement of amino acid sequences on codon-anticodon residues in proteins, which can cause some mutations in humans.

Specific replacement of Q base in the anticodon of tRNA by guanine catalyzed by a cell-free extract of rabbit reticulocytes.

PubMed Central

Okada, N; Harada, F; Nishimura, S

1976-01-01

Guanylation of tRNA by a lysate of rabbit reticulocytes was reported previously by Farkas and Singh. This reaction was investigated further using 18 purified E. coli tRNAs as acceptors.Results showed that only tRNATyr, tRNAHis, tRNAAsn and tRNAAsp which contain the modified nucleoside Q in the anticodon acted as acceptors. Analysis of the nucleotide sequences in the guanylated tRNA showed that guanine specifically replaced Q base in these tRNAs. Images PMID:792816

The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription.

PubMed Central

Ke, N; Gao, X; Keeney, J B; Boeke, J D; Voytas, D F

1999-01-01

Retrotransposons and retroviruses replicate by reverse transcription of an mRNA intermediate. Most retroelements initiate reverse transcription from a host-encoded tRNA primer. DNA synthesis typically extends from the 3'-OH of the acceptor stem, which is complementary to sequences on the retroelement mRNA (the primer binding site, PBS). However, for some retrotransposons, including the yeast Ty5 elements, sequences in the anticodon stem-loop of the initiator methionine tRNA (IMT) are complementary to the PBS. We took advantage of the genetic tractability of the yeast system to investigate the mechanism of Ty5 priming. We found that transposition frequencies decreased at least 800-fold for mutations in the Ty5 PBS that disrupt complementarity with the IMT. Similarly, transposition was reduced at least 200-fold for IMT mutations in the anticodon stem-loop. Base pairing between the Ty5 PBS and IMT is essential for transposition, as compensatory changes that restored base pairing between the two mutant RNAs restored transposition significantly. An analysis of 12 imt mutants with base changes outside of the region of complementarity failed to identify other tRNA residues important for transposition. In addition, assays carried out with heterologous IMTs from Schizosaccharomyces pombe and Arabidopsis thaliana indicated that residues outside of the anticodon stem-loop have at most a fivefold effect on transposition. Our genetic system should make it possible to further define the components required for priming and to understand the mechanism by which Ty5's novel primer is generated. PMID:10411136

tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast.

PubMed

Klassen, Roland; Ciftci, Akif; Funk, Johanna; Bruch, Alexander; Butter, Falk; Schaffrath, Raffael

2016-12-15

Using budding yeast, we investigated a negative interaction network among genes for tRNA modifications previously implicated in anticodon-codon interaction: 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm 5 s 2 U34: ELP3, URM1), pseudouridine (Ψ38/39: DEG1) and cyclic N6-threonyl-carbamoyl-adenosine (ct 6 A37: TCD1). In line with functional cross talk between these modifications, we find that combined removal of either ct 6 A37 or Ψ38/39 and mcm 5 U34 or s 2 U34 results in morphologically altered cells with synthetic growth defects. Phenotypic suppression by tRNA overexpression suggests that these defects are caused by malfunction of tRNA Lys UUU or tRNA Gln UUG , respectively. Indeed, mRNA translation and synthesis of the Gln-rich prion Rnq1 are severely impaired in the absence of Ψ38/39 and mcm 5 U34 or s 2 U34, and this defect can be rescued by overexpression of tRNA Gln UUG Surprisingly, we find that combined modification defects in the anticodon loops of different tRNAs induce similar cell polarity- and nuclear segregation defects that are accompanied by increased aggregation of cellular proteins. Since conditional expression of an artificial aggregation-prone protein triggered similar cytological aberrancies, protein aggregation is likely responsible for loss of morphogenesis and cytokinesis control in mutants with inappropriate tRNA anticodon loop modifications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Aminoacyl-tRNA synthetases database Y2K

PubMed Central

Szymanski, Maciej; Barciszewski, Jan

2000-01-01

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html PMID:10592262

Aminoacyl-tRNA synthetases database Y2K.

PubMed

Szymanski, M; Barciszewski, J

2000-01-01

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html

Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.

PubMed Central

Yokoyama, S; Watanabe, T; Murao, K; Ishikura, H; Yamaizumi, Z; Nishimura, S; Miyazawa, T

1985-01-01

Proton NMR analyses have been made to elucidate the conformational characteristics of modified nucleotides as found in the first position of the anticodon of tRNA [derivatives of 5-methyl-2-thiouridine 5'-monophosphate (pxm5s2U) and derivatives of 5-hydroxyuridine 5'-monophosphate (pxo5U)]. In pxm5s2U, the C3'-endo form is extraordinarily more stable than the C2'-endo form for the ribose ring, because of the combined effects of the 2-thiocarbonyl group and the 5-substituent. By contrast, in pxo5U, the C2'-endo form is much more stable than the C3'-endo form, because of the interaction between the 5-substituent and the 5'-phosphate group. The enthalpy differences between the C2'-endo form and the C3'-endo form have been obtained as 1.1, -0.7, and 0.1 kcal/mol (1 cal = 4.184 J) for pxm5s2U, pxo5U, and unmodified uridine 5'-monophosphate, respectively. These findings lead to the conclusion that xm5s2U in the first position of the anticodon exclusively takes the C3'-endo form to recognize adenosine (but not uridine) as the third letter of the codon, whereas xo5U takes the C2'-endo form as well as the C3'-endo form to recognize adenosine, guanosine, and uridine as the third letter of the codon on ribosome. Accordingly, the biological significance of such modifications of uridine to xm5s2U/xo5U is in the regulation of the conformational rigidity/flexibility in the first position of the anticodon so as to guarantee the correct and efficient translation of codons in protein biosynthesis. PMID:3860833

YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase.

PubMed

Harris, Kimberly A; Jones, Victoria; Bilbille, Yann; Swairjo, Manal A; Agris, Paul F

2011-09-01

The post-transcriptional nucleoside modifications of tRNA's anticodon domain form the loop structure and dynamics required for effective and accurate recognition of synonymous codons. The N(6)-threonylcarbamoyladenosine modification at position 37 (t(6)A(37)), 3'-adjacent to the anticodon, of many tRNA species in all organisms ensures the accurate recognition of ANN codons by increasing codon affinity, enhancing ribosome binding, and maintaining the reading frame. However, biosynthesis of this complex modification is only partially understood. The synthesis requires ATP, free threonine, a single carbon source for the carbamoyl, and an enzyme yet to be identified. Recently, the universal protein family Sua5/YciO/YrdC was associated with t(6)A(37) biosynthesis. To further investigate the role of YrdC in t(6)A(37) biosynthesis, the interaction of the Escherichia coli YrdC with a heptadecamer anticodon stem and loop of lysine tRNA (ASL(Lys)(UUU)) was examined. YrdC bound the unmodified ASL(Lys)(UUU) with high affinity compared with the t(6)A(37)-modified ASL(Lys)(UUU) (K(d) = 0.27 ± 0.20 μM and 1.36 ± 0.39 μM, respectively). YrdC also demonstrated specificity toward the unmodified versus modified anticodon pentamer UUUUA and toward threonine and ATP. The protein did not significantly alter the ASL architecture, nor was it able to base flip A(37), as determined by NMR, circular dichroism, and fluorescence of 2-aminopuine at position 37. Thus, current data support the hypothesis that YrdC, with many of the properties of a putative threonylcarbamoyl transferase, most likely functions as a component of a heteromultimeric protein complex for t(6)A(37) biosynthesis.

tRNA wobble modifications and protein homeostasis

PubMed Central

Ranjan, Namit; Rodnina, Marina V.

2016-01-01

Abstract tRNA is a central component of the protein synthesis machinery in the cell. In living cells, tRNAs undergo numerous post-transcriptional modifications. In particular, modifications at the anticodon loop play an important role in ensuring efficient protein synthesis, maintaining protein homeostasis, and helping cell adaptation and survival. Hypo-modification of the wobble position of the tRNA anticodon loop is of particular relevance for translation regulation and is implicated in various human diseases. In this review we summarize recent evidence of how methyl and thiol modifications in eukaryotic tRNA at position 34 affect cellular fitness and modulate regulatory circuits at normal conditions and under stress. PMID:27335723

Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid

PubMed Central

Kwon, Inchan; Choi, Eun Sil

2016-01-01

Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation. PMID:27028506

Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid.

PubMed

Kwon, Inchan; Choi, Eun Sil

2016-01-01

Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation.

One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

PubMed Central

Rodin, Andrei S; Szathmáry, Eörs; Rodin, Sergei N

2009-01-01

Background The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II) that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1) ribozymic precursors of the synthetases seem to have used the same two sterically mirror modes of tRNA recognition, (2) having these two modes might have helped in preventing erroneous aminoacylation of ancestral tRNAs with complementary anticodons, yet (3) the risk of confusion for the presumably earliest pairs of complementarily encoded amino acids had little to do with anticodons. Accordingly, in this communication we focus on the acceptor stem. Results Our main result is the emergence of a palindrome structure for the acceptor stem's common ancestor, reconstructed from the phylogenetic trees of Bacteria, Archaea and Eukarya. In parallel, for pairs of ancestral tRNAs with complementary anticodons, we present updated evidence of concerted complementarity of the second bases in the acceptor stems. These two results suggest that the first pairs of "complementary" amino acids that were engaged in primordial coding, such as Gly and Ala, could have avoided erroneous aminoacylation if and only if the acceptor stems of their adaptors were recognized from the same, major groove, side. The class II protein synthetases then inherited this "primary preference" from isofunctional ribozymes. Conclusion Taken together, our results support the hypothesis that the genetic code per se (the one associated with the anticodons) and the operational code of aminoacylation (associated with the acceptor) diverged from a common ancestor that probably began developing before translation. The primordial advantage of linking some amino acids (most likely glycine and alanine) to the ancestral acceptor stem may have been selective retention in a protocell surrounded by a leaky membrane for use in nucleotide and coenzyme synthesis. Such acceptor stems (as cofactors) thus transferred amino acids as groups for biosynthesis. Later, with the advent of an anticodon loop, some amino acids (such as aspartic acid, histidine, arginine) assumed a catalytic role while bound to such extended adaptors, in line with the original coding coenzyme handle (CCH) hypothesis. Reviewers This article was reviewed by Rob Knight, Juergen Brosius and Anthony Poole. PMID:19173731

Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment.

PubMed

Biddle, Wil; Schmitt, Margaret A; Fisk, John D

2016-12-01

Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNA Opt We suspected a modification of the tRNA Opt AUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNA Opt AUG is converted to inosine. We identified tRNA Opt AUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

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

2012-10-01

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

Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism.

PubMed

Vendeix, Franck A P; Murphy, Frank V; Cantara, William A; Leszczyńska, Grażyna; Gustilo, Estella M; Sproat, Brian; Malkiewicz, Andrzej; Agris, Paul F

2012-03-02

Human tRNA(Lys3)(UUU) (htRNA(Lys3)(UUU)) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 2-methylthio-N(6)-threonylcarbamoyladenosine (ms(2)t(6)A(37)), and pseudouridine (Ψ(39)) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39)). Ribosome binding assays in vitro revealed that the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound AAA and AAG codons, whereas binding of the unmodified ASL(Lys3)(UUU) was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ(39) enhanced the thermodynamic stability of the ASL through base stacking while ms(2)t(6)A(37) restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm(5)s(2)U(34) and ms(2)t(6)A(37) participate in the stability of the anticodon-codon interaction. Importantly, the mcm(5)s(2)U(34)·G(3) wobble base pair is in the Watson-Crick geometry, requiring unusual hydrogen bonding to G in which mcm(5)s(2)U(34) must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evolution of Protein Synthesis from an RNA World

PubMed Central

Noller, Harry F.

2012-01-01

SUMMARY Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World. Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Second, it is proposed that the decoding site of the ribosome evolved from a mechanism for duplication of RNA. This process involved homodimeric “duplicator RNAs,” resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template. PMID:20610545

Replacement of RNA hairpins by in vitro selected tetranucleotides.

PubMed Central

Dichtl, B; Pan, T; DiRenzo, A B; Uhlenbeck, O C

1993-01-01

An in vitro selection method based on the autolytic cleavage of yeast tRNA(Phe) by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides. Based on the rates of the site-specific cleavage by Pb2+ and the presence of a specific UV-induced crosslink, certain tetranucleotide sequences allow proper folding of the rest of the tRNA molecule, whereas others do not. One such successful tetramer sequence was also used to replace the acceptor stem of yeast tRNA(Phe) and the anticodon hairpin of E.coli tRNA(Phe) without disrupting folding. These experiments suggest that certain tetramers may be able to replace structurally nonessential hairpins in any RNA. Images PMID:7680121

Effects of tRNA modification on translational accuracy depend on intrinsic codon-anticodon strength.

PubMed

Manickam, Nandini; Joshi, Kartikeya; Bhatt, Monika J; Farabaugh, Philip J

2016-02-29

Cellular health and growth requires protein synthesis to be both efficient to ensure sufficient production, and accurate to avoid producing defective or unstable proteins. The background of misreading error frequency by individual tRNAs is as low as 2 × 10(-6) per codon but is codon-specific with some error frequencies above 10(-3) per codon. Here we test the effect on error frequency of blocking post-transcriptional modifications of the anticodon loops of four tRNAs in Escherichia coli. We find two types of responses to removing modification. Blocking modification of tRNA(UUC)(Glu) and tRNA(QUC)(Asp) increases errors, suggesting that the modifications act at least in part to maintain accuracy. Blocking even identical modifications of tRNA(UUU)(Lys) and tRNA(QUA)(Tyr) has the opposite effect of decreasing errors. One explanation could be that the modifications play opposite roles in modulating misreading by the two classes of tRNAs. Given available evidence that modifications help preorder the anticodon to allow it to recognize the codons, however, the simpler explanation is that unmodified 'weak' tRNAs decode too inefficiently to compete against cognate tRNAs that normally decode target codons, which would reduce the frequency of misreading. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.

PubMed

McCrate, Nina E; Varner, Mychel E; Kim, Kenneth I; Nagan, Maria C

2006-01-01

Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA(Lys,3)UUU three modified bases are present in the anticodon stem-loop--2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine (psi) at position 39--two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human tRNA(Lys,3)UUU [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390-13395]. Molecular dynamics simulations of nine tRNA anticodon stem-loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to psi39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.

Complexes of polyadenylic acid and the methyl esters of amino acids

NASA Technical Reports Server (NTRS)

Khaled, M. A.; Mulins, D. W., Jr.; Swindle, M.; Lacey, J. C., Jr.

1983-01-01

A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

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

PubMed

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

2013-02-01

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

Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672

Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine

PubMed Central

Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Russell, Susan P.; Krivos, Kady; Castleberry, Colette M.; Blum, Paul; Limbach, Patrick A.; Söll, Dieter; RajBhandary, Uttam L.

2010-01-01

Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle () of bacteria and archaea is essential for this tRNA to read the isoleucine codon AUA and to differentiate between AUA and the methionine codon AUG. To identify the modified cytidine in archaea, we have purified this tRNA species from Haloarcula marismortui, established its codon reading properties, used liquid chromatography–mass spectrometry (LC-MS) to map RNase A and T1 digestion products onto the tRNA, and used LC-MS/MS to sequence the oligonucleotides in RNase A digests. These analyses revealed that the modification of cytidine in the anticodon of adds 112 mass units to its molecular mass and makes the glycosidic bond unusually labile during mass spectral analyses. Accurate mass LC-MS and LC-MS/MS analysis of total nucleoside digests of the demonstrated the absence in the modified cytidine of the C2-oxo group and its replacement by agmatine (decarboxy-arginine) through a secondary amine linkage. We propose the name agmatidine, abbreviation C+, for this modified cytidine. Agmatidine is also present in Methanococcus maripaludis and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNAIle of euryarchaea and crenarchaea. The identification of agmatidine shows that bacteria and archaea have developed very similar strategies for reading the isoleucine codon AUA while discriminating against the methionine codon AUG. PMID:20133752

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

PubMed Central

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

2013-01-01

The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNALys3. Host cell tRNALys is selectively packaged into HIV-1 through a specific interaction between the major tRNALys-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNALys3 is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNALys and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNALys3 in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNALys to increase the efficiency of tRNALys3 annealing to viral RNA. PMID:23264568

Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA

PubMed Central

Théobald-Dietrich, Anne; Frugier, Magali; Giegé, Richard; Rudinger-Thirion, Joëlle

2004-01-01

The newly discovered tRNAPyl is involved in specific incorporation of pyrrolysine in the active site of methylamine methyltransferases in the archaeon Methanosarcina barkeri. In solution probing experiments, a transcript derived from tRNAPyl displays a secondary fold slightly different from the canonical cloverleaf and interestingly similar to that of bovine mitochondrial tRNASer(uga). Aminoacylation of tRNAPyl transcript by a typical class II synthetase, LysRS from yeast, was possible when its amber anticodon CUA was mutated into a lysine UUU anticodon. Hydrolysis protection assays show that lysylated tRNAPyl can be recognized by bacterial elongation factor. This indicates that no antideterminant sequence is present in the body of the tRNAPyl transcript to prevent it from interacting with EF-Tu, in contrast with the otherwise functionally similar tRNASec that mediates selenocysteine incorporation. PMID:14872064

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach.

PubMed

Kamble, Asmita S; Fandilolu, Prayagraj M; Sambhare, Susmit B; Sonawane, Kailas D

2017-01-01

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by 'wobble' as well as a novel 'single' hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at ‘wobble’ position in anticodon loop of tRNALeu: A molecular modeling approach

PubMed Central

Kamble, Asmita S.; Fandilolu, Prayagraj M.; Sambhare, Susmit B.; Sonawane, Kailas D.

2017-01-01

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by ‘wobble’ as well as a novel ‘single’ hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons. PMID:28453549

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

PubMed Central

Cardoso Guimarães, Romeu

2017-01-01

The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes—structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process—anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don’t accumulate to saturation, which would trigger inhibition. PMID:28383509

Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNAIle

PubMed Central

Montanari, Arianna; De Luca, Cristina; Di Micco, Patrizio; Morea, Veronica; Frontali, Laura; Francisci, Silvia

2011-01-01

Previous work has demonstrated the usefulness of the yeast model to investigate the molecular mechanisms underlying defects due to base substitutions in mitochondrial tRNA genes, and to identify suppressing molecules endowed with potential clinical relevance. The present paper extends these investigations to two human equivalent yeast mutations located at positions 32 and 33 in the anticodon loop of tRNAIle. Notwithstanding the proximity of the two T>C base substitutions, the effects of these mutations have been found to be quite different in yeast, as they are in human. The T32C substitution has a very severe effect in yeast, consisting in a complete inhibition of growth on nonfermentable substrates. Conversely, respiratory defects caused by the T33C mutation could only be observed in a defined genetic context. Analyses of available sequences and selected tRNA three-dimensional structures were performed to provide explanations for the different behavior of these adjacent mutations. Examination of the effects of previously identified suppressors demonstrated that overexpression of the TUF1 gene did not rescue the defective phenotypes determined by either mutation, possibly as a consequence of the lack of interactions between EF-Tu and the tRNA anticodon arm in known structures. On the contrary, both the cognate IleRS and the noncognate LeuRS and ValRS are endowed with suppressing activities toward both mutations. This allows us to extend to the tRNAIle mutants the cross-suppression activity of aminoacyl-tRNA synthetases previously demonstrated for tRNALeu and tRNAVal mutants. PMID:21914842

A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index

PubMed Central

Xia, Xuhua

2015-01-01

Two alternative hypotheses attribute different benefits to codon-anticodon adaptation. The first assumes that protein production is rate limited by both initiation and elongation and that codon-anticodon adaptation would result in higher elongation efficiency and more efficient and accurate protein production, especially for highly expressed genes. The second claims that protein production is rate limited only by initiation efficiency but that improved codon adaptation and, consequently, increased elongation efficiency have the benefit of increasing ribosomal availability for global translation. To test these hypotheses, a recent study engineered a synthetic library of 154 genes, all encoding the same protein but differing in degrees of codon adaptation, to quantify the effect of differential codon adaptation on protein production in Escherichia coli. The surprising conclusion that “codon bias did not correlate with gene expression” and that “translation initiation, not elongation, is rate-limiting for gene expression” contradicts the conclusion reached by many other empirical studies. In this paper, I resolve the contradiction by reanalyzing the data from the 154 sequences. I demonstrate that translation elongation accounts for about 17% of total variation in protein production and that the previous conclusion is due to the use of a codon adaptation index (CAI) that does not account for the mutation bias in characterizing codon adaptation. The effect of translation elongation becomes undetectable only when translation initiation is unrealistically slow. A new index of translation elongation ITE is formulated to facilitate studies on the efficiency and evolution of the translation machinery. PMID:25480780

Loss of Anticodon Wobble Uridine Modifications Affects tRNALys Function and Protein Levels in Saccharomyces cerevisiae

PubMed Central

Klassen, Roland; Grunewald, Pia; Thüring, Kathrin L.; Eichler, Christian; Helm, Mark; Schaffrath, Raffael

2015-01-01

In eukaryotes, wobble uridines in the anticodons of tRNALys UUU, tRNAGlu UUC and tRNAGln UUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNALys UUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNALys UUU hypomodification and malfunction. PMID:25747122

Loss of anticodon wobble uridine modifications affects tRNA(Lys) function and protein levels in Saccharomyces cerevisiae.

PubMed

Klassen, Roland; Grunewald, Pia; Thüring, Kathrin L; Eichler, Christian; Helm, Mark; Schaffrath, Raffael

2015-01-01

In eukaryotes, wobble uridines in the anticodons of tRNA(Lys)UUU, tRNA(Glu)UUC and tRNA(Gln)UUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNA(Lys)UUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNA(Lys)UUU hypomodification and malfunction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vendeix, Franck A.P.; Murphy, IV, Frank V.; Cantara, William A.

Human tRNA Lys3 UUU (htRNA Lys3 UUU) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm 5s 2U 34), 2-methylthio-N 6-threonylcarbamoyladenosine (ms 2t 6A 37), and pseudouridine (Ψ 39) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASLmore » Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37;Ψ 39). Ribosome binding assays in vitro revealed that the hASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37;Ψ 39 bound AAA and AAG codons, whereas binding of the unmodified ASL Lys3 UUU was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ 39 enhanced the thermodynamic stability of the ASL through base stacking while ms 2t 6A 37 restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37;Ψ 39 bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm 5s 2U 34 and ms 2t 6A 37 participate in the stability of the anticodon–codon interaction. Importantly, the mcm 5s 2U 34·G 3 wobble base pair is in the Watson–Crick geometry, requiring unusual hydrogen bonding to G in which mcm 5s 2U 34 must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.« less

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

PubMed

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

2018-03-13

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

Amino acid signature enables proteins to recognize modified tRNA.

PubMed

Spears, Jessica L; Xiao, Xingqing; Hall, Carol K; Agris, Paul F

2014-02-25

Human tRNA(Lys3)UUU is the primer for HIV replication. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNA(Lys3)UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNA(Lys3)UUU is post-transcriptionally modified, but until recently, the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N(6)-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNA(Lys3)UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and assisted model building with energy refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic) that recognized the tRNA's fully modified anticodon stem and loop domain, hASL(Lys3)UUU. Peptides of this sequence specifically recognized and bound modified htRNA(Lys3)UUU with an affinity 10-fold higher than that of the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology as well as biochemistry to explore RNA binding proteins and to inhibit those protein functions.

Independent suppression of ribosomal +1 frameshifts by different tRNA anticodon loop modifications.

PubMed

Klassen, Roland; Bruch, Alexander; Schaffrath, Raffael

2017-09-02

Recently, a role for the anticodon wobble uridine modification 5-methoxycarbonylmethyl-2-thiouridine (mcm 5 s 2 U) has been revealed in the suppression of translational +1 frameshifts in Saccharomyces cerevisiae. Loss of either the mcm 5 U or s 2 U parts of the modification elevated +1 frameshift rates and results obtained with reporters involving a tRNA Lys UUU dependent frameshift site suggested these effects are caused by reduced ribosomal A-site binding of the hypomodified tRNA. Combined loss of mcm 5 U and s 2 U leads to increased ribosome pausing at tRNA Lys UUU dependent codons and synergistic growth defects but effects on +1 frameshift rates remained undefined to this end. We show in here that simultaneous removal of mcm 5 U and s 2 U results in synergistically increased +1 frameshift rates that are suppressible by extra copies of tRNA Lys UUU . Thus, two distinct chemical modifications of the same wobble base independently contribute to reading frame maintenance, loss of which may cause or contribute to observed growth defects. Since the thiolation pathway is sensitive to moderately elevated temperatures in yeast, we observe a heat-induced increase of +1 frameshift rates in wild type cells that depends on the sulfur transfer protein Urm1. Furthermore, we find that temperature-induced frameshifting is kept in check by the dehydration of N6-threonylcarbamoyladenosine (t 6 A) to its cyclic derivative (ct 6 A) at the anticodon adjacent position 37. Since loss of ct 6 A in elp3 or urm1 mutant cells is detrimental for temperature stress resistance we assume that conversion of t 6 A to ct 6 A serves to limit deleterious effects on translational fidelity caused by hypomodified states of wobble uridine bases.

Problem-Solving Test: The Effect of Synonymous Codons on Gene Expression

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2009-01-01

Terms to be familiar with before you start to solve the test: the genetic code, codon, degenerate codons, protein synthesis, aminoacyl-tRNA, anticodon, antiparallel orientation, wobble, unambiguous codons, ribosomes, initiation, elongation and termination of translation, peptidyl transferase, translocation, degenerate oligonucleotides, green…

RNA repair: an antidote to cytotoxic eukaryal RNA damage.

PubMed

Nandakumar, Jayakrishnan; Schwer, Beate; Schaffrath, Raffael; Shuman, Stewart

2008-07-25

RNA healing and sealing enzymes drive informational and stress response pathways entailing repair of programmed 2',3' cyclic PO(4)/5'-OH breaks. Fungal, plant, and phage tRNA ligases use different strategies to discriminate the purposefully broken ends of the anticodon loop. Whereas phage ligase recognizes the tRNA fold, yeast and plant ligases do not and are instead hardwired to seal only the tRNA 3'-OH, 2'-PO(4) ends formed by healing of a cyclic phosphate. tRNA anticodon damage inflicted by secreted ribotoxins such as fungal gamma-toxin underlies a rudimentary innate immune system. Yeast cells are susceptible to gamma-toxin because the sealing domain of yeast tRNA ligase is unable to rectify a break at the modified wobble base of tRNA(Glu(UUC)). Plant andphage tRNA repair enzymes protect yeast from gamma-toxin because they are able to reverse the damage. Our studies underscore how a ribotoxin exploits an Achilles' heel in the target cell's tRNA repair system.

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

PubMed

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

2017-08-16

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

Biochemical and Structures Studies of tRNA Modificaton and Repair Enzymes

ERIC Educational Resources Information Center

Zhou, Chun

2009-01-01

RNA hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. We first determined the crystal structures of "Pseudomonas aeruginosa" DMATase.…

Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

PubMed

Seligmann, Hervé

2018-05-01

Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections. Copyright © 2018 Elsevier B.V. All rights reserved.

Structures and functions of proteins and nucleic acids in protein biosynthesis

NASA Astrophysics Data System (ADS)

Miyazawa, Tatsuo; Yokoyama, Shigeyuki

Infrared and Raman spectroscopy is useful for studying helical conformations of polypeptides, which are determined by molecular structure parameters. Nuclear magnetic resonance spectroscopy, as well as X-ray analysis, is now established to be important for conformation studies of proteins and nucleic acids in solution. This article is mainly concerned with the conformational aspect and function regulation in protein biosynthesis. The strict recognition of transfer ribonucleic acid (tRNA) by aminoacyl-tRNA synthetase (ARS) is achieved by multi-step mutual adaptation. The conformations of ARS-bound amino acids have been elucidated by transferred nuclear Overhauser effect analysis. Aminoacyl-tRNA takes the 3‧-isomeric form in the polypeptide chain elongation cycle. The regulation of codon recognition by post-transcriptional modification is achieved by conversion of the conformational characteristic of the anticodon of tRNA. The cytidine → lysidine modification of the anticodon of minor isoleucine tRNA concurrently converts the amino acid specificity and the codon specificity. As novel protein engineering, a basic strategy has been established for in vivo biosynthesis of proteins that are substituted with unnatural amino acids (alloproteins).

TTA codons in some genes prevent their expression in a class of developmental, antibiotic-negative, Streptomyces mutants.

PubMed Central

Leskiw, B K; Lawlor, E J; Fernandez-Abalos, J M; Chater, K F

1991-01-01

In Streptomyces coelicolor A3(2) and the related species Streptomyces lividans 66, aerial mycelium formation and antibiotic production are blocked by mutations in bldA, which specifies a tRNA(Leu)-like gene product which would recognize the UUA codon. Here we show that phenotypic expression of three disparate genes (carB, lacZ, and ampC) containing TTA codons depends strongly on bldA. Site-directed mutagenesis of carB, changing its two TTA codons to CTC (leucine) codons, resulted in bldA-independent expression; hence the bldA product is the principal tRNA for the UUA codon. Two other genes (hyg and aad) containing TTA codons show a medium-dependent reduction in phenotypic expression (hygromycin resistance and spectinomycin resistance, respectively) in bldA mutants. For hyg, evidence is presented that the UUA codon is probably being translated by a tRNA with an imperfectly matched anticodon, giving very low levels of gene product but relatively high resistance to hygromycin. It is proposed that TTA codons may be generally absent from genes expressed during vegetative growth and from the structural genes for differentiation and antibiotic production but present in some regulatory and resistance genes associated with the latter processes. The codon may therefore play a role in developmental regulation. Images PMID:1826053

Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp).

PubMed Central

Przykorska, A; el Adlouni, C; Keith, G; Szarkowski, J W; Dirheimer, G

1992-01-01

A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions. Images PMID:1542562

S-Geranyl-2-thiouridine wobble nucleosides of bacterial tRNAs; chemical and enzymatic synthesis of S-geranylated-RNAs and their physicochemical characterization

PubMed Central

Sierant, Malgorzata; Leszczynska, Grazyna; Sadowska, Klaudia; Dziergowska, Agnieszka; Rozanski, Michal; Sochacka, Elzbieta; Nawrot, Barbara

2016-01-01

Recently, highly lipophilic S-geranylated derivatives of 5-methylaminomethyl-2-thiouridine (mnm5geS2U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm5geS2U) were found at the first (wobble) anticodon position in bacterial tRNAs specific for Lys, Glu and Gln. The function and cellular biogenesis of these unique tRNAs remain poorly understood. Here, we present one direct and two post-synthetic chemical routes for preparing model geS2U-RNAs. Our experimental data demonstrate that geS2U-RNAs are more lipophilic than their parent S2U-RNAs as well as non-modified U-RNAs. Thermodynamic studies revealed that the S-geranyl-2-thiouridine-containing RNA has higher affinity toward complementary RNA strand with G opposite the modified unit than with A. Recombinant tRNA selenouridine synthase (SelU) exhibits sulfur-specific geranylation activity toward model S2U-RNA, which is composed of the anticodon-stem-loop (ASL) from the human tRNALys3 sequence. In addition, the presence of magnesium ions is required to achieve appreciable geranylation efficiencies. PMID:27566149

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

PubMed

Wei, Fangping; Chen, Bowen

2012-03-01

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

Modulating Transfer RNA Anticodon Modifications and Biologic Responses in Human Cells.

DTIC Science & Technology

1987-12-15

mercaptopurine and 6-ethylmercaptopurine were both able to inhibit the growth and induce functional differentiation of HGPRT-deficient HL-60 cells...with 6-ethylmercaptopurine mediating these responses at significantly lower concentrations than 6- mercaptopurine . In contrast to 6- mercaptopurine , 6...concentrations it was cytotoxic to both. The mechanism by which 6-ethyl- mercaptopurine elicits its effects on HL-60 cells remains to be established

Three-dimensional structure of Escherichia coli initiator tRNA/f//Met/

NASA Technical Reports Server (NTRS)

Woo, N. H.; Rich, A.; Roe, B. A.

1980-01-01

The crystal structure of Escherichia coli tRNA(f)(Met), an initiator transfer RNA, has been determined. While grossly similar to that of the chain-elongating yeast tRNA(Phe), there are three major differences. One involves the folding of the anticodon loop; in particular, the position of the constant uridine, U33. This difference was unexpected and may be of functional significance.

Synthesis, base pairing and structure studies of geranylated RNA

PubMed Central

Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V.; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

2016-01-01

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium. The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNAGluUUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon–anticodon interaction during ribosome binding. PMID:27307604

Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N 6-threonylcarbamoyladenosine TcdA Function.

PubMed

Fernández, Francisco J; Gómez, Sara; Navas-Yuste, Sergio; López-Estepa, Miguel; Vega, M Cristina

2017-06-21

We demonstrate methods for the expression and purification of tRNA(UUU) in Escherichia coli and the analysis by gel retardation assays of the binding of tRNA(UUU) to TcdA, an N 6 -threonylcarbamoyladenosine (t 6 A) dehydratase, which cyclizes the threonylcarbamoyl side chain attached to A37 in the anticodon stem loop (ASL) of tRNAs to cyclic t 6 A (ct 6 A). Transcription of the synthetic gene encoding tRNA(UUU) is induced in E. coli with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and the cells containing tRNA are harvested 24 h post-induction. The RNA fraction is purified using the acid phenol extraction method. Pure tRNA is obtained by a gel filtration chromatography that efficiently separates the small-sized tRNA molecules from larger intact or fragmented nucleic acids. To analyze TcdA binding to tRNA(UUU), TcdA is mixed with tRNA(UUU) and separated on a native agarose gel at 4 °C. The free tRNA(UUU) migrates faster, while the TcdA-tRNA(UUU) complexes undergo a mobility retardation that can be observed upon staining of the gel. We demonstrate that TcdA is a tRNA(UUU)-binding enzyme. This gel retardation assay can be used to study TcdA mutants and the effects of additives and other proteins on binding.

Recognition of Culex Bidens Dyar and Culex Interfor Dyar (Diptera: Culicidae) as Separate Species

DTIC Science & Technology

1986-01-01

genitalia. ARGENTINA. Corrientes : locality not specified, 6 specimens. Jujuy: Ledesma, 1 specimen. Santa fe: Calchaqui’, 1 specimen; Humboldt, 2 specimens...close to surface of lateral plate. MATERIAL EXAHINED: 42 male genitalia. ARGENTINA. Chaco: locality not specified, 2 specimens. Corrientes

The Chern-Simons Current in Systems of DNA-RNA Transcriptions

NASA Astrophysics Data System (ADS)

Capozziello, Salvatore; Pincak, Richard; Kanjamapornkul, Kabin; Saridakis, Emmanuel N.

2018-04-01

A Chern-Simons current, coming from ghost and anti-ghost fields of supersymmetry theory, can be used to define a spectrum of gene expression in new time series data where a spinor field, as alternative representation of a gene, is adopted instead of using the standard alphabet sequence of bases $A, T, C, G, U$. After a general discussion on the use of supersymmetry in biological systems, we give examples of the use of supersymmetry for living organism, discuss the codon and anti-codon ghost fields and develop an algebraic construction for the trash DNA, the DNA area which does not seem active in biological systems. As a general result, all hidden states of codon can be computed by Chern-Simons 3 forms. Finally, we plot a time series of genetic variations of viral glycoprotein gene and host T-cell receptor gene by using a gene tensor correlation network related to the Chern-Simons current. An empirical analysis of genetic shift, in host cell receptor genes with separated cluster of gene and genetic drift in viral gene, is obtained by using a tensor correlation plot over time series data derived as the empirical mode decomposition of Chern-Simons current.

Amino acid fermentation at the origin of the genetic code.

PubMed

de Vladar, Harold P

2012-02-10

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

47 CFR 73.610 - Minimum distance separations between stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... they fail to comply with the requirements specified in paragraphs (b), (c) and (d) of this section... separation. (c) Minimum allotment and station adjacent channel separations applicable to all zones: (1... pairs of channels (see § 73.603(a)). (d) In addition to the requirements of paragraphs (a), (b) and (c...

12 CFR 37.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... deficiency is added to, the unpaid balance of the amount financed. (b) Bank means a national bank and a... credit from that bank upon the occurrence of a specified event. The agreement may be separate from or a... to repay an extension of credit from that bank upon the occurrence of a specified event. The...

12 CFR 37.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... deficiency is added to, the unpaid balance of the amount financed. (b) Bank means a national bank and a... credit from that bank upon the occurrence of a specified event. The agreement may be separate from or a... to repay an extension of credit from that bank upon the occurrence of a specified event. The...

12 CFR 37.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... deficiency is added to, the unpaid balance of the amount financed. (b) Bank means a national bank and a... credit from that bank upon the occurrence of a specified event. The agreement may be separate from or a... to repay an extension of credit from that bank upon the occurrence of a specified event. The...

12 CFR 37.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... deficiency is added to, the unpaid balance of the amount financed. (b) Bank means a national bank and a... credit from that bank upon the occurrence of a specified event. The agreement may be separate from or a... to repay an extension of credit from that bank upon the occurrence of a specified event. The...

12 CFR 37.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... deficiency is added to, the unpaid balance of the amount financed. (b) Bank means a national bank and a... credit from that bank upon the occurrence of a specified event. The agreement may be separate from or a... to repay an extension of credit from that bank upon the occurrence of a specified event. The...

Synthesis, base pairing and structure studies of geranylated RNA.

PubMed

Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

2016-07-27

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA(Glu) UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed Central

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

2009-01-01

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

The complete mitochondrial genome of the onychophoran Epiperipatus biolleyi reveals a unique transfer RNA set and provides further support for the ecdysozoa hypothesis.

PubMed

Podsiadlowski, Lars; Braband, Anke; Mayer, Georg

2008-01-01

Onychophora (velvet worms) play a crucial role in current discussions on position of arthropods. The ongoing Articulata/Ecdysozoa debate is in need of additional ground pattern characters for Panarthropoda (Arthropoda, Tardigrada, and Onychophora). Hence, Onychophora is an important outgroup taxon in resolving the relationships among arthropods, irrespective of whether morphological or molecular data are used. To date, there has been a noticeable lack of mitochondrial genome data from onychophorans. Here, we present the first complete mitochondrial genome sequence of an onychophoran, Epiperipatus biolleyi (Peripatidae), which shows several characteristic features. Specifically, the gene order is considerably different from that in other arthropods and other bilaterians. In addition, there is a lack of 9 tRNA genes usually present in bilaterian mitochondrial genomes. All these missing tRNAs have anticodon sequences corresponding to 4-fold degenerate codons, whereas the persisting 13 tRNAs all have anticodons pairing with 2-fold degenerate codons. Sequence-based phylogenetic analysis of the mitochondrial protein-coding genes provides a robust support for a clade consisting of Onychophora, Priapulida, and Arthropoda, which confirms the Ecdysozoa hypothesis. However, resolution of the internal ecdysozoan relationships suffers from a cluster of long-branching taxa (including Nematoda and Platyhelminthes) and a lack of data from Tardigrada and further nemathelminth taxa in addition to nematodes and priapulids.

rRNA fragmentation induced by a yeast killer toxin.

PubMed

Kast, Alene; Klassen, Roland; Meinhardt, Friedhelm

2014-02-01

Virus like dsDNA elements (VLE) in yeast were previously shown to encode the killer toxins PaT and zymocin, which target distinct tRNA species via specific anticodon nuclease (ACNase) activities. Here, we characterize a third member of the VLE-encoded toxins, PiT from Pichia inositovora, and identify PiOrf4 as the cytotoxic subunit by conditional expression in Saccharomyces cerevisiae. In contrast to the tRNA targeting toxins, however, neither a change of the wobble uridine modification status by introduction of elp3 or trm9 mutations nor tRNA overexpression rescued from PiOrf4 toxicity. Consistent with a distinct RNA target, expression of PiOrf4 causes specific fragmentation of the 25S and 18S rRNA. A stable cleavage product comprising the first ∼ 130 nucleotides of the 18S rRNA was purified and characterized by linker ligation and subsequent reverse transcription; 3'-termini were mapped to nucleotide 131 and 132 of the 18S rRNA sequence, a region showing some similarity to the anticodon loop of tRNA(Glu)(UUC), the zymocin target. PiOrf4 residues Glu9 and His214, corresponding to catalytic sites Glu9 and His209 in the ACNase subunit of zymocin are essential for in vivo toxicity and rRNA fragmentation, raising the possibility of functionally conserved RNase modules in both proteins. © 2013 John Wiley & Sons Ltd.

Separating duff and litter for improved mass and carbon estimates

Treesearch

David Chojnacky; Michael Amacher; Michael Gavazzi

2009-01-01

Mass and carbon load estimates, such as those from forest soil organic matter (duff and litter), inform forestry decisions. The US Forest Inventory and Analysis (FIA) Program systematically collects data nationwide: a down woody material protocol specifies discrete duff and litter depth measurements, and a soils protocol specifies mass and carbon of duff and litter...

NPDES Permit for Air Force Academy Municipal Separate Storm Sewer System in Colorado

EPA Pesticide Factsheets

Under NPDES permit CO-R042007, the U.S. Air Force Academy is authorized to discharge from all municipal separate storm sewer system outfalls to the receiving waters specified in the permit in El Paso County, Colorado.

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

The functional requirements to be met by the HAL/S-FC compiler, and the hardware and software compatibilities between the compiler system and the environment in which it operates are defined. Associated runtime facilities and the interface with the Software Development Laboratory are specified. The construction of the HAL/S-FC system as functionally separate units and the interfaces between those units is described. An overview of the system's capabilities is presented and the hardware/operating system requirements are specified. The computer-dependent aspects of the HAL/S-FC are also specified. Compiler directives are included.

NPDES Permit for Denver VA Hospital Municipal Separate Storm Sewer System in Colorado

EPA Pesticide Factsheets

Under NPDES permit CO-R042008, the Veterans Administration (Medical Center, Denver Campus) is authorized to discharge from all municipal separate storm sewer system outfalls to the receiving waters specified in the permit in the City of Denver, Colorado.

Exposure of a liquefied gas container to an external fire.

PubMed

Raj, Phani K

2005-06-30

In liquefied gas, bulk-storage facilities and plants, the separation distances between storage tanks and between a tank and a line of adjoining property that can be built are governed by local regulations and/or codes (e.g. National Fire Protection Association (NFPA) 58, 2004). Separation distance requirements have been in the NFPA 58 Code for over 60 years; however, no scientific foundations (either theoretical or experimental) are available for the specified distances. Even though the liquefied petroleum gas (LPG) industry has operated safely over the years, there is a question as to whether the code-specified distances provide sufficient safety to LPG-storage tanks, when they are exposed to large external fires. A radiation heat-transfer-based model is presented in this paper. The temporal variation of the vapor-wetted tank-wall temperature is calculated when exposed to thermal radiation from an external, non-impinging, large, 30.5 m (100 ft) diameter, highly radiative, hydrocarbon fuel (pool) fire located at a specified distance. Structural steel wall of a pressurized, liquefied gas container (such as the ASME LP-Gas tank) begins to lose its strength, when the wall temperature approaches a critical temperature, 810 K (1000 degrees F). LP-Gas tank walls reaching close to this temperature will be a cause for major concern because of increased potential for tank failure, which could result in catastrophic consequences. Results from the model for exposure of different size ASME (LP-Gas) containers to a hydrocarbon pool fire of 30.5 m (100 ft) in diameter, located with its base edge at the separation distances specified by NFPA 58 [NFPA 58, Liquefied Petroleum Gas Code, Table 6.3.1, 2004 ed., National Fire Protection Association, Quincy, MA, 2004] indicate that the vapor-wetted wall temperature of the containers never reach the critical temperature under common wind conditions (0, 5 and 10 m/s), with the flame tilting towards the tank. This indicates that the separation distances specified in the code are adequate for non-impingement type of fires. The model can be used to test the efficacy of other similar codes and regulations for other materials.

Two inviscid computational simulations of separated flow about airfoils

NASA Technical Reports Server (NTRS)

Barnwell, R. W.

1976-01-01

Two inviscid computational simulations of separated flow about airfoils are described. The basic computational method is the line relaxation finite-difference method. Viscous separation is approximated with inviscid free-streamline separation. The point of separation is specified, and the pressure in the separation region is calculated. In the first simulation, the empiricism of constant pressure in the separation region is employed. This empiricism is easier to implement with the present method than with singularity methods. In the second simulation, acoustic theory is used to determine the pressure in the separation region. The results of both simulations are compared with experiment.

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

PubMed Central

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-01-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. PMID:27197221

Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family.

PubMed

Zallot, Rémi; Brochier-Armanet, Céline; Gaston, Kirk W; Forouhar, Farhad; Limbach, Patrick A; Hunt, John F; de Crécy-Lagard, Valérie

2014-08-15

Queuosine (Q) is a modification found at the wobble position of tRNAs with GUN anticodons. Although Q is present in most eukaryotes and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or microflora, making q an important but under-recognized micronutrient for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases (eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous accessory subunit (QTRTD1) forming a complex that catalyzes q insertion into target tRNAs. Phylogenetic analysis of eTGT subunits revealed a patchy distribution pattern in which gene losses occurred independently in different clades. Searches for genes co-distributing with eTGT family members identified DUF2419 as a potential Q salvage protein family. This prediction was experimentally validated in Schizosaccharomyces pombe by confirming that Q was present by analyzing tRNA(Asp) with anticodon GUC purified from wild-type cells and by showing that Q was absent from strains carrying deletions in the QTRT1 or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya with a few possible cases of horizontal gene transfer to bacteria. The universality of the DUF2419 function was confirmed by complementing the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues. The enzymatic function of this family is yet to be determined, but structural similarity with DNA glycosidases suggests a ribonucleoside hydrolase activity.

Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications.

PubMed

Wang, Zheng-Liang; Li, Chao; Fang, Wen-Yuan; Yu, Xiao-Ping

2016-09-30

The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders. Copyright © 2016 Elsevier B.V. All rights reserved.

A GTPase reaction accompanying the rejection of Leu-tRNA2 by UUU-programmed ribosomes. Proofreading of the codon-anticodon interaction by ribosomes.

PubMed

Thompson, R C; Dix, D B; Gerson, R B; Karim, A M

1981-01-10

The characteristics of a GTPase reaction between poly(U)-programmed ribosomes, EFTu . GTP, and the near-cognate aminoacyl (aa)-tRNA, Leu-tRNA Leu 2, have been studied to assess the role of this reaction in proofreading of the codon-anticodon interaction. The reaction resembles the GTPase reaction with cognate aa-tRNAs and EFTu . GTP in its substrate requirements, in its involving EFTu . GTP . aa-tRNA ternary complexes, and in its requiring a free ribosomal A-site. The noncognate reaction differs from the cognate one in that aa-tRNA becomes stably bound to the ribosomes only 5% of the time; it therefore seems best characterized as an abortive enzymatic binding reaction. The rate of reaction is a significant fraction (4%) of that of the cognate aa-tRNA, indicating that recognition of ternary complexes by ribosomes involves a level of error greater than that of translation as a whole. The rejection of the noncognate aa-tRNA following GTP hydrolysis is therefore a vital step in the translation process and fulfills the criteria set for a proofreading reaction. Leu-tRNA Leu 2 which escapes rejection through proofreading, forms a stable complex with the ribosomal A-site, so it appears that the Leu-tRNA2 which was rejected never reached the A-site and that proofreading precedes full A-site binding.

Military Transition Assistance Program (TAP): An Overview

DTIC Science & Technology

2017-03-15

Title II of P.L. 112-56) which made a pre-separation counseling program mandatory for all servicemembers who have served at least 180 continuous days...anticipated retirement date or 12-month period preceding the anticipated separation date. It also specifies that pre-separation counseling should...in the development, management oversight, and strategic planning of TAP. TAP Counseling Requirements Over time, Congress has increased the

40 CFR 63.137 - Process wastewater provisions-oil-water separators.

Code of Federal Regulations, 2010 CFR

2010-07-01

... separators. 63.137 Section 63.137 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... for other emission variables such as temperature and barometric pressure, or (ii) An engineering...)(1) and the schedule specified in paragraphs (c)(1) and (c)(2) of this section. (1) Measurement of...

Trajectory Specification for High-Capacity Air Traffic Control

NASA Technical Reports Server (NTRS)

Paielli, Russell A.

2004-01-01

In the current air traffic management system, the fundamental limitation on airspace capacity is the cognitive ability of human air traffic controllers to maintain safe separation with high reliability. The doubling or tripling of airspace capacity that will be needed over the next couple of decades will require that tactical separation be at least partially automated. Standardized conflict-free four-dimensional trajectory assignment will be needed to accomplish that objective. A trajectory specification format based on the Extensible Markup Language is proposed for that purpose. This format can be used to downlink a trajectory request, which can then be checked on the ground for conflicts and approved or modified, if necessary, then uplinked as the assigned trajectory. The horizontal path is specified as a series of geodetic waypoints connected by great circles, and the great-circle segments are connected by turns of specified radius. Vertical profiles for climb and descent are specified as low-order polynomial functions of along-track position, which is itself specified as a function of time. Flight technical error tolerances in the along-track, cross-track, and vertical axes define a bounding space around the reference trajectory, and conformance will guarantee the required separation for a period of time known as the conflict time horizon. An important safety benefit of this regimen is that the traffic will be able to fly free of conflicts for at least several minutes even if all ground systems and the entire communication infrastructure fail. Periodic updates in the along-track axis will adjust for errors in the predicted along-track winds.

Amino acid fermentation at the origin of the genetic code

PubMed Central

2012-01-01

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eörs Szathmáry (nominated by Dr. Gáspár Jékely) and Dr. Ádám Kun (nominated by Dr. Sandor Pongor) PMID:22325238

Functional recognition of the modified human tRNALys3(UUU) anticodon domain by HIV's nucleocapsid protein and a peptide mimic.

PubMed

Graham, William D; Barley-Maloney, Lise; Stark, Caren J; Kaur, Amarpreet; Stolarchuk, Christina; Stolyarchuk, Khrystyna; Sproat, Brian; Leszczynska, Grazyna; Malkiewicz, Andrzej; Safwat, Nedal; Mucha, Piotr; Guenther, Richard; Agris, Paul F

2011-07-22

The HIV-1 nucleocapsid protein, NCp7, facilitates the use of human tRNA(Lys3)(UUU) as the primer for reverse transcription. NCp7 also remodels the htRNA's amino acid accepting stem and anticodon domains in preparation for their being annealed to the viral genome. To understand the possible influence of the htRNA's unique composition of post-transcriptional modifications on NCp7 recognition of htRNA(Lys3)(UUU), the protein's binding and functional remodeling of the human anticodon stem and loop domain (hASL(Lys3)) were studied. NCp7 bound the hASL(Lys3)(UUU) modified with 5-methoxycarbonylmethyl-2-thiouridine at position-34 (mcm(5)s(2)U(34)) and 2-methylthio-N(6)-threonylcarbamoyladenosine at position-37 (ms(2)t(6)A(37)) with a considerably higher affinity than the unmodified hASL(Lys3)(UUU) (K(d)=0.28±0.03 and 2.30±0.62 μM, respectively). NCp7 denatured the structure of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) more effectively than that of the unmodified hASL(Lys3)(UUU). Two 15 amino acid peptides selected from phage display libraries demonstrated a high affinity (average K(d)=0.55±0.10 μM) and specificity for the ASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37) comparable to that of NCp7. The peptides recognized a t(6)A(37)-modified ASL with an affinity (K(d)=0.60±0.09 μM) comparable to that for hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37), indicating a preference for the t(6)A(37) modification. Significantly, one of the peptides was capable of relaxing the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) structure in a manner similar to that of NCp7, and therefore could be used to further study protein recognition of RNA modifications. The post-transcriptional modifications of htRNA(Lys3)(UUU) have been found to be important determinants of NCp7's recognition prior to the tRNA(Lys3)(UUU) being annealed to the viral genome as the primer of reverse transcription. Copyright © 2011 Elsevier Ltd. All rights reserved.

The nucleotide sequence of a major glycine transfer RNA from the posterior silk gland of Bombyx mori L.

PubMed Central

Zúñiga, M C; Steitz, J A

1977-01-01

The nucleotide sequence of tRNA1Gly isolated from the posterior silk gland of Bombyx mori has been determined. This transfer RNA is present in high amounts in the posterior silk gland during the fifth larval instar. It has a GCC anticodon, capable of decoding a major glycine codon in the fibroin messenger RNA, GGU. Structural features of Bombyx tRNA1Gly and its homology to other eukaryotic glycine tRNAs are discussed. Images PMID:414206

75 FR 76317 - Airworthiness Directives; Gulfstream Aerospace LP (Type Certificate Previously Held by Israel...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-08

... an unsafe condition on an aviation product. The MCAI describes the unsafe condition as: Sponge rubber... condition for the specified products. The MCAI states: Sponge rubber padding used to provide separation... to correct improper separation and removing sponge rubber padding, and repair or replacement of any...

77 FR 44432 - Airworthiness Directives; Gulfstream Aerospace LP (Type Certificate Previously Held by Israel...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-30

... Westwind Astra, and Gulfstream 100 airplanes. This AD was prompted by a report indicating that sponge... inspecting for the presence of sponge rubber padding and for proper separation of the fuel lines and... specified products. The MCAI states: Sponge rubber padding used to provide separation between wheel well...

A Practical Approach to Replication of Abstract Data Objects

DTIC Science & Technology

1990-05-01

rigorous torture testing. Torture testing was done with the aid of a basher program that allows the user to configure an object and perform a specified...number of transactions, each containing a specified number of operations on the object. There are separate basher programs for RSMs and MRSMs. The...modify the object (Writes and Erases, for RSMs). The basher maintains a local, non- replicated table that tracks the RSM that is under test. Each

Exposure-Focused Family-Based CBT for Youth With ASD and Comorbid Anxiety

ClinicalTrials.gov

2017-10-25

Autism; Asperger's Syndrome; Pervasive Developmental Disorder Not Otherwise Specified; Generalized Anxiety Disorder; Social Phobia; Separation Anxiety Disorder; Obsessive-compulsive Disorder; Specific Phobia

Psychotherapy for Anxiety in Children With Autism Spectrum Disorder

ClinicalTrials.gov

2017-11-30

Autism Spectrum Disorders; Autism; Asperger's Syndrome; Pervasive Developmental Disability - Not Otherwise Specified; Obsessive-compulsive Disorder; Social Phobia; Generalized Anxiety Disorder; Specific Phobia; Separation Anxiety Disorder

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

PubMed

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-07-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. © 2016 Mühlhausen et al.; Published by Cold Spring Harbor Laboratory Press.

Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity

PubMed Central

López, Ana; Castelló, María José; Gil, María José; Zheng, Bo; Chen, Peng; Vera, Pablo

2015-01-01

tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2´-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response. PMID:26492405

Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification.

PubMed

Pichard-Kostuch, Adeline; Zhang, Wenhua; Liger, Dominique; Daugeron, Marie-Claire; Letoquart, Juliette; Li de la Sierra-Gallay, Ines; Forterre, Patrick; Collinet, Bruno; van Tilbeurgh, Herman; Basta, Tamara

2018-04-12

N6-threonyl-carbamoyl adenosine (t6A) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G or C). t6A stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of t6A, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function. In the present study, we report structure-function analysis of Pyrococcus abyssi Sua5 (Pa-Sua5). Crystallographic data revealed binding sites for bicarbonate substrate and pyrophosphate product. The linker of Pa-Sua5 forms a loop structure that folds into the active site gorge and closes it. Using structure-guided mutational analysis we established that the conserved sequence motifs in the linker and the domain-domain interface are essential for the function of Pa-Sua5. We propose that the linker participates actively in the biosynthesis of TC-AMP by binding to ATP/PPi and by stabilizing the N-carboxy-L-threonine intermediate. Hence, TsaC orthologs which lack such a linker and SUA5 domain use different mechanism for TC-AMP synthesis. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans.

PubMed

Bacusmo, Jo Marie; Orsini, Silvia S; Hu, Jennifer; DeMott, Michael; Thiaville, Patrick C; Elfarash, Ameer; Paulines, Mellie June; Rojas-Benítez, Diego; Meineke, Birthe; Deutsch, Chris; Iwata-Reuyl, Dirk; Limbach, Patrick A; Dedon, Peter C; Rice, Kelly C; Shuman, Stewart; Crécy-Lagard, Valérie de

2017-07-20

Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNA Lys UUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t 6 A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t 6 A-deficient yeast derivatives, it is shown that t 6 A is a positive determinant for PrrC proteins from various bacterial species. Streptococcus mutans is one of the few bacteria where the t 6 A synthesis gene tsaE (brpB) is dispensable and its genome encodes a PrrC toxin. We had previously shown using an HPLC-based assay that the S. mutans tsaE mutant was devoid of t 6 A. However, we describe here a novel and a more sensitive hybridization-based t 6 A detection method (compared to HPLC) that showed t 6 A was still present in the S. mutans ΔtsaE, albeit at greatly reduced levels (93% reduced compared with WT). Moreover, mutants in 2 other S. mutans t 6 A synthesis genes (tsaB and tsaC) were shown to be totally devoid of the modification thus confirming its dispensability in this organism. Furthermore, analysis of t 6 A modification ratios and of t 6 A synthesis genes mRNA levels in S. mutans suggest they may be regulated by growth phase.

Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine

PubMed Central

Zhang, Yan; Wang, Lei; Schultz, Peter G.; Wilson, Ian A.

2005-01-01

The Methanococcus jannaschii tRNATyr/TyrRS pair has been engineered to incorporate unnatural amino acids into proteins in E. coli. To reveal the structural basis for the altered specificity of mutant TyrRS for O-methyl-l-tyrosine (OMeTyr), the crystal structures for the apo wild-type and mutant M. jannaschii TyrRS were determined at 2.66 and 3.0 Å, respectively, for comparison with the published structure of TyrRS complexed with tRNATyr and substrate tyrosine. A large conformational change was found for the anticodon recognition loop 257–263 of wild-type TyrRS upon tRNA binding in order to facilitate recognition of G34 of the anticodon loop through π-stacking and hydrogen bonding interactions. Loop 133–143, which is close to the tRNA acceptor stem-binding site, also appears to be stabilized by interaction with the tRNATyr. Binding of the substrate tyrosine results in subtle and cooperative movements of the side chains within the tyrosine-binding pocket. In the OMeTyr-specific mutant synthetase structure, the signature motif KMSKS loop and acceptor stem-binding loop 133–143 were surprisingly ordered in the absence of bound ATP and tRNA. The active-site mutations result in altered hydrogen bonding and steric interactions which favor binding of OMeTyr over l-tyrosine. The structure of the mutant and wild-type TyrRS now provide a basis for generating new active-site libraries to evolve synthetases specific for other unnatural amino acids. PMID:15840835

A new flow model for highly separated airfoil flows at low speeds

NASA Technical Reports Server (NTRS)

Zumwalt, G. W.; Naik, S. N.

1979-01-01

An analytical model for separated airfoil flows is presented which is based on experimentally observed physical phenomena. These include a free stagnation point aft of the airfoil and a standing vortex in the separated region. A computer program is described which iteratively matches the outer potential flow, the airfoil turbulent boundary layer, the separated jet entrainment, mass conservation in the separated bubble, and the rear stagnation pressure. Separation location and pressure are not specified a priori. Results are presented for surface pressure coefficient and compared with experiment for three angles of attack for a GA(W)-1, 17% thick airfoil.

Optimum instantaneous impulsive orbital injection to attain a specified asymptotic velocity vector.

NASA Technical Reports Server (NTRS)

Bean, W. C.

1971-01-01

A nalysis of the necessary conditions of Battin for instantaneous orbital injection, with consideration of the uniqueness of his solution, and of the further problem which arises in the degenerate case when radius vector and asymptotic vector are separated by 180 deg. It is shown that when the angular separation between radius vector and asymptotic velocity vector satisfies theta not equal to 180 deg, there are precisely two insertion-velocity vectors which permit attainment of the target asymptotic velocity vector, one yielding posigrade, the other retrograde motion. When theta equals to 180 deg, there is a family of insertion-velocity vectors which permit attainment of a specified asymptotic velocity vector with a unique insertion-velocity vector for every arbitrary orientation of a target unit angular momentum vector.

14 CFR 29.783 - Doors.

Code of Federal Regulations, 2010 CFR

2010-01-01

... passenger doors and for preventing their opening in flight inadvertently or as a result of mechanical... specified in paragraph (d) of this section, acting separately relative to the surrounding structure. (2) The...

14 CFR 29.783 - Doors.

Code of Federal Regulations, 2013 CFR

2013-01-01

... passenger doors and for preventing their opening in flight inadvertently or as a result of mechanical... specified in paragraph (d) of this section, acting separately relative to the surrounding structure. (2) The...

40 CFR 80.1463 - What penalties apply under the RFS program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... subject to a civil penalty as specified in sections 205 and 211(d) of the Clean Air Act, for every day of... subject to a separate day of violation for each day in the compliance period. (c) Any person liable under... subpart is liable for a separate day of violation for each day such a requirement remains unfulfilled. [75...

Photo-dependent protein biosynthesis using a caged aminoacyl-tRNA.

PubMed

Akahoshi, Akiya; Doi, Yoshio; Sisido, Masahiko; Watanabe, Kazunori; Ohtsuki, Takashi

2014-12-01

Translation systems with four-base codons provide a powerful strategy for protein engineering and protein studies because they enable site-specific incorporation of non-natural amino acids into proteins. In this study, a caged aminoacyl-tRNA with a four-base anticodon was synthesized. The caged aminoacyl-tRNA contains a photocleavable nitroveratryloxycarbonyl (NVOC) group. This study showed that the caged aminoacyl-tRNA was not deacylated, did not bind to EF-Tu, and was activated by light. Photo-dependent translation of an mRNA containing the four-base codon was demonstrated using the caged aminoacyl-tRNA.

Couplings of character and of chirality in the origin of the genetic system

NASA Technical Reports Server (NTRS)

Lacey, J. C. Jr; Wickramasinghe, N. S.; Cook, G. W.; Anderson, G.; Lacey JC, J. r. (Principal Investigator)

1993-01-01

Data from the literature and new data presented here suggest that the genetic system (coding and protein synthesis) is based on relationships of character and structure between amino acids and nucleic acids. Character relationships seem to be anticodonic and structurally the greatest preferences are seen between the heteropair, L-amino acids and D-ribose nucleic acids. However, living systems using the other heteropair must have been equally likely. Homopairing (L-L and D-D) in living systems seems unlikely. Awareness of the heterocoupling of steric forms narrows somewhat the problem of understanding the origin of chirality.

Evolution of specifier proteins in glucosinolate-containing plants

PubMed Central

2012-01-01

Background The glucosinolate-myrosinase system is an activated chemical defense system found in plants of the Brassicales order. Glucosinolates are stored separately from their hydrolytic enzymes, the myrosinases, in plant tissues. Upon tissue damage, e.g. by herbivory, glucosinolates and myrosinases get mixed and glucosinolates are broken down to an array of biologically active compounds of which isothiocyanates are toxic to a wide range of organisms. Specifier proteins occur in some, but not all glucosinolate-containing plants and promote the formation of biologically active non-isothiocyanate products upon myrosinase-catalyzed glucosinolate breakdown. Results Based on a phytochemical screening among representatives of the Brassicales order, we selected candidate species for identification of specifier protein cDNAs. We identified ten specifier proteins from a range of species of the Brassicaceae and assigned each of them to one of the three specifier protein types (NSP, nitrile-specifier protein, ESP, epithiospecifier protein, TFP, thiocyanate-forming protein) after heterologous expression in Escherichia coli. Together with nine known specifier proteins and three putative specifier proteins found in databases, we subjected the newly identified specifier proteins to phylogenetic analyses. Specifier proteins formed three major clusters, named AtNSP5-cluster, AtNSP1-cluster, and ESP/TFP cluster. Within the ESP/TFP cluster, specifier proteins grouped according to the Brassicaceae lineage they were identified from. Non-synonymous vs. synonymous substitution rate ratios suggested purifying selection to act on specifier protein genes. Conclusions Among specifier proteins, NSPs represent the ancestral activity. The data support a monophyletic origin of ESPs from NSPs. The split between NSPs and ESPs/TFPs happened before the radiation of the core Brassicaceae. Future analyses have to show if TFP activity evolved from ESPs at least twice independently in different Brassicaceae lineages as suggested by the phylogeny. The ability to form non-isothiocyanate products by specifier protein activity may provide plants with a selective advantage. The evolution of specifier proteins in the Brassicaceae demonstrates the plasticity of secondary metabolism within an activated plant defense system. PMID:22839361

Multiple Microcomputer Control Algorithm.

DTIC Science & Technology

1979-09-01

discrete and semaphore supervisor calls can be used with tasks in separate processors, in which case they are maintained in shared memory. Operations on ...the source or destination operand specifier of each mode in most cases . However, four of the 16 general register addressing modes and one of the 8 pro...instruction time is based on the specified usage factors and the best cast, and worst case execution times for the instruc- 1I 5 1NAVTRAEQZJ1PCrN M’.V7~j

Thin-layer approximation and algebraic model for separated turbulent flows

NASA Technical Reports Server (NTRS)

Baldwin, B.; Lomax, H.

1978-01-01

An algebraic turbulence model for two- and three-dimensional separated flows is specified that avoids the necessity for finding the edge of the boundary layer. Properties of the model are determined and comparisons made with experiment for an incident shock on a flat plate, separated flow over a compression corner, and transonic flow over an airfoil. Separation and reattachment points from numerical Navier-Stokes solutions agree with experiment within one boundary-layer thickness. Use of law-of-the-wall boundary conditions does not alter the predictions significantly. Applications of the model to other cases are contained in companion papers.

50 CFR 648.120 - Catch quotas and other restrictions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Limit (ACL). (a) The Scup Monitoring Committee shall recommend to the MAFMC separate ACLs for the... frequently exceeded. (2) The MAFMC may specify more frequent or more specific ACL performance review criteria...

Dimensions of vegetable parenting practices among preschoolers.

PubMed

Baranowski, Tom; Chen, Tzu-An; O'Connor, Teresia; Hughes, Sheryl; Beltran, Alicia; Frankel, Leslie; Diep, Cassandra; Baranowski, Janice C

2013-10-01

The objective of this study was to determine the factor structure of 31 effective and ineffective vegetable parenting practices used by parents of preschool children based on three theoretically proposed factors: responsiveness, control and structure. The methods employed included both corrected item-total correlations and confirmatory factor analysis. Acceptable fit was obtained only when effective and ineffective parenting practices were analyzed separately. Among effective items the model included one second order factor (effectiveness) and the three proposed first order factors. The same structure was revealed among ineffective items, but required correlated paths be specified among items. A theoretically specified three factor structure was obtained among 31 vegetable parenting practice items, but likely to be effective and ineffective items had to be analyzed separately. Research is needed on how these parenting practices factors predict child vegetable intake. Copyright © 2013 Elsevier Ltd. All rights reserved.

PYROCHEMICAL DECONTAMINATION METHOD FOR REACTOR FUEL

DOEpatents

Buyers, A.G.

1959-06-30

A pyro-chemical method is presented for decontaminating neutron irradiated uranium and separating plutonium therefrom by contact in the molten state with a metal chloride salt. Uranium trichloride and uranium tetrachloride either alone or in admixture with alkaline metal and alkaline eanth metal fluorides under specified temperature and specified phase ratio conditions extract substantially all of the uranium from the irradiated uranium fuel together with certain fission products. The phases are then separated leaving purified uranium metal. The uranium and plutonium in the salt phase can be reduced to forin a highly decontaminated uraniumplutonium alloy. The present method possesses advantages for economically decontaminating irradiated nuclear fuel elements since irradiated fuel may be proccessed immediately after withdrawal from the reactor and the uranium need not be dissolved and later reduced to the metallic form. Accordingly, the uranium may be economically refabricated and reinserted into the reactor.

Coordinating structural and functional synapse development: postsynaptic p21-activated kinase independently specifies glutamate receptor abundance and postsynaptic morphology.

PubMed

Albin, Stephanie D; Davis, Graeme W

2004-08-04

Here, we show that postsynaptic p21-activated kinase (Pak) signaling diverges into two genetically separable pathways at the Drosophila neuromuscular junction. One pathway controls glutamate receptor abundance. Pak signaling within this pathway is specified by a required interaction with the adaptor protein Dreadlocks (Dock). We demonstrate that Dock is localized to the synapse via an Src homology 2-mediated protein interaction. Dock is not necessary for Pak localization but is necessary to restrict Pak signaling to control glutamate receptor abundance. A second genetically separable function of Pak kinase signaling controls muscle membrane specialization through the regulation of synaptic Discs-large. In this pathway, Dock is dispensable. We present a model in which divergent Pak signaling is able to coordinate two different features of postsynaptic maturation, receptor abundance, and muscle membrane specialization.

75 FR 70101 - Airworthiness Directives; Sikorsky Aircraft Corporation (Sikorsky) Model S-70A and S-70C Helicopters

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-17

... test (UT) inspection of the tail gearbox output bevel gear (gear) for a crack. If you find a crack... gear cracking incidents, one of which resulted in the tail rotor separating from the helicopter. The actions specified by this AD are intended to detect a crack in the gear to prevent a tail rotor separating...

JPRS Report (Erratum), Science & Technology, Japan, Selections from MITI White Paper on Industrial Technology Trends and Issues

DTIC Science & Technology

1989-08-30

year period in the following products: Technology Field Product New materials Composite materials Amorphous alloys Macromolecule separation...plastics 8. Composite materials B. Parts 9. Optical fiber 10. Semiconductor lasers 11. CCD 12. Semiconductor memory elements 13. Microcomputers...separation. Composite materials (containing carbon fiber) (1) Aerospace users required strict specifi cations for carbon fiber, resulting in

Land Vehicle Tire Qualification

DTIC Science & Technology

2009-03-25

Bead damage / separation -Severe open splices and/or liner separations - Tire induced loss of air -Exposed or broken casing -Bulges in tread or...sidewall SAE J2014 11 SAE J2014 4.14 Tire Treadlife Durability -10000 miles duration -Evaluate tread wear performance of candidate tire -Measurements at... Tread Depth measurement of reference and candidate tires taken at specified intervals • Candidate tires must complete the test and tread wear projections

The origin and evolution of tRNA inferred from phylogenetic analysis of structure.

PubMed

Sun, Feng-Jie; Caetano-Anollés, Gustavo

2008-01-01

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TPsiC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TPsiC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures.

2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver.

PubMed Central

Païs de Barros, J P; Keith, G; El Adlouni, C; Glasser, A L; Mack, G; Dirheimer, G; Desgrès, J

1996-01-01

The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals. PMID:8628682

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

PubMed Central

2011-01-01

Background The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. Results A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Conclusions Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS. PMID:21486489

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers.

PubMed

Gao, Lei; Zhou, Yuan; Wang, Zhi-Wei; Su, Ying-Juan; Wang, Ting

2011-04-13

The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.

Determinants of the cytotoxicity of PrrC anticodon nuclease and its amelioration by tRNA repair

PubMed Central

Meineke, Birthe; Shuman, Stewart

2012-01-01

Breakage of tRNALys(UUU) by the Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection that is ultimately thwarted by a virus-encoded RNA repair system. PrrC homologs are prevalent in other bacteria, but their activities and substrates are not defined. We find that induced expression of EcoPrrC is toxic in Saccharomyces cerevisiae and E. coli, whereas the Neisseria meningitidis PrrC (NmePrrC) is not. PrrCs consist of an N-terminal NTPase module and a C-terminal nuclease module. Domain swaps identified the EcoPrrC nuclease domain as decisive for toxicity when linked to either the Eco or Nme NTPase. Indeed, a single arginine-to-tryptophan change in the NmePrrC nuclease domain (R316W) educed a gain-of-function and rendered NmePrrC toxic to yeast, with genetic evidence for tRNALys(UUU) being the relevant target. The reciprocal Trp-to-Arg change in EcoPrrC (W335R) abolished its toxicity. Further mutagenesis of the EcoPrrC nuclease domain highlighted an ensemble of 15 essential residues and distinguished between hypomorphic alleles and potential nuclease-nulls. We report that the RNA repair phase of the bacterial virus-host dynamic is also portable to yeast, where coexpression of the T4 enzymes Pnkp and Rnl1 ameliorated the toxicity of NmePrrC-R316W. Plant tRNA ligase AtRNL also countered NmePrrC-R316W toxicity, in a manner that depended on AtRNL's 5′-kinase and ligase functions. PMID:22101242

Determinants of the cytotoxicity of PrrC anticodon nuclease and its amelioration by tRNA repair.

PubMed

Meineke, Birthe; Shuman, Stewart

2012-01-01

Breakage of tRNA(Lys(UUU)) by the Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection that is ultimately thwarted by a virus-encoded RNA repair system. PrrC homologs are prevalent in other bacteria, but their activities and substrates are not defined. We find that induced expression of EcoPrrC is toxic in Saccharomyces cerevisiae and E. coli, whereas the Neisseria meningitidis PrrC (NmePrrC) is not. PrrCs consist of an N-terminal NTPase module and a C-terminal nuclease module. Domain swaps identified the EcoPrrC nuclease domain as decisive for toxicity when linked to either the Eco or Nme NTPase. Indeed, a single arginine-to-tryptophan change in the NmePrrC nuclease domain (R316W) educed a gain-of-function and rendered NmePrrC toxic to yeast, with genetic evidence for tRNA(Lys(UUU)) being the relevant target. The reciprocal Trp-to-Arg change in EcoPrrC (W335R) abolished its toxicity. Further mutagenesis of the EcoPrrC nuclease domain highlighted an ensemble of 15 essential residues and distinguished between hypomorphic alleles and potential nuclease-nulls. We report that the RNA repair phase of the bacterial virus-host dynamic is also portable to yeast, where coexpression of the T4 enzymes Pnkp and Rnl1 ameliorated the toxicity of NmePrrC-R316W. Plant tRNA ligase AtRNL also countered NmePrrC-R316W toxicity, in a manner that depended on AtRNL's 5'-kinase and ligase functions.

50 CFR 648.140 - Catch quotas and other restrictions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Catch Limit (ACL). (a) The Black Sea Bass Monitoring Committee shall recommend to the MAFMC separate... MAFMC may specify more frequent or more specific ACL performance review criteria as part of a stock...

45 CFR 301.1 - General definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Child Support Enforcement which is the separate organizational unit within the Department with the... Welfare Regulations Relating to Public Welfare OFFICE OF CHILD SUPPORT ENFORCEMENT (CHILD SUPPORT... 66 percent. Assigned support obligation means, unless otherwise specified, any support obligation...

Co-Optimization of Blunt Body Shapes for Moving Vehicles

NASA Technical Reports Server (NTRS)

Kinney, David J. (Inventor); Mansour, Nagi N (Inventor); Brown, James L. (Inventor); Garcia, Joseph A (Inventor); Bowles, Jeffrey V (Inventor)

2014-01-01

A method and associated system for multi-disciplinary optimization of various parameters associated with a space vehicle that experiences aerocapture and atmospheric entry in a specified atmosphere. In one embodiment, simultaneous maximization of a ratio of landed payload to vehicle atmospheric entry mass, maximization of fluid flow distance before flow separation from vehicle, and minimization of heat transfer to the vehicle are performed with respect to vehicle surface geometric parameters, and aerostructure and aerothermal vehicle response for the vehicle moving along a specified trajectory. A Pareto Optimal set of superior performance parameters is identified.

Response-specifying cue for action interferes with perception of feature-sharing stimuli.

PubMed

Nishimura, Akio; Yokosawa, Kazuhiko

2010-06-01

Perceiving a visual stimulus is more difficult when a to-be-executed action is compatible with that stimulus, which is known as blindness to response-compatible stimuli. The present study explored how the factors constituting the action event (i.e., response-specifying cue, response intention, and response feature) affect the occurrence of this blindness effect. The response-specifying cue varied along the horizontal and vertical dimensions, while the response buttons were arranged diagonally. Participants responded based on one dimension randomly determined in a trial-by-trial manner. The response intention varied along a single dimension, whereas the response location and the response-specifying cue varied within both vertical and horizontal dimensions simultaneously. Moreover, the compatibility between the visual stimulus and the response location and the compatibility between that stimulus and the response-specifying cue was separately determined. The blindness effect emerged exclusively based on the feature correspondence between the response-specifying cue of the action task and the visual target of the perceptual task. The size of this stimulus-stimulus (S-S) blindness effect did not differ significantly across conditions, showing no effect of response intention and response location. This finding emphasizes the effect of stimulus factors, rather than response factors, of the action event as a source of the blindness to response-compatible stimuli.

Time delay spectrum conditioner

DOEpatents

Greiner, Norman R.

1980-01-01

A device for delaying specified frequencies of a multiple frequency laser beam. The device separates the multiple frequency beam into a series of spatially separated single frequency beams. The propagation distance of the single frequency beam is subsequently altered to provide the desired delay for each specific frequency. Focusing reflectors can be utilized to provide a simple but nonadjustable system or, flat reflectors with collimating and focusing optics can be utilized to provide an adjustable system.

The numerical calculation of laminar boundary-layer separation

NASA Technical Reports Server (NTRS)

Klineberg, J. M.; Steger, J. L.

1974-01-01

Iterative finite-difference techniques are developed for integrating the boundary-layer equations, without approximation, through a region of reversed flow. The numerical procedures are used to calculate incompressible laminar separated flows and to investigate the conditions for regular behavior at the point of separation. Regular flows are shown to be characterized by an integrable saddle-type singularity that makes it difficult to obtain numerical solutions which pass continuously into the separated region. The singularity is removed and continuous solutions ensured by specifying the wall shear distribution and computing the pressure gradient as part of the solution. Calculated results are presented for several separated flows and the accuracy of the method is verified. A computer program listing and complete solution case are included.

RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay.

PubMed

Dean, Kimberly M; Grayhack, Elizabeth J

2012-12-01

We have developed a robust and sensitive method, called RNA-ID, to screen for cis-regulatory sequences in RNA using fluorescence-activated cell sorting (FACS) of yeast cells bearing a reporter in which expression of both superfolder green fluorescent protein (GFP) and yeast codon-optimized mCherry red fluorescent protein (RFP) is driven by the bidirectional GAL1,10 promoter. This method recapitulates previously reported progressive inhibition of translation mediated by increasing numbers of CGA codon pairs, and restoration of expression by introduction of a tRNA with an anticodon that base pairs exactly with the CGA codon. This method also reproduces effects of paromomycin and context on stop codon read-through. Five key features of this method contribute to its effectiveness as a selection for regulatory sequences: The system exhibits greater than a 250-fold dynamic range, a quantitative and dose-dependent response to known inhibitory sequences, exquisite resolution that allows nearly complete physical separation of distinct populations, and a reproducible signal between different cells transformed with the identical reporter, all of which are coupled with simple methods involving ligation-independent cloning, to create large libraries. Moreover, we provide evidence that there are sequences within a 9-nt library that cause reduced GFP fluorescence, suggesting that there are novel cis-regulatory sequences to be found even in this short sequence space. This method is widely applicable to the study of both RNA-mediated and codon-mediated effects on expression.

Game-theoretic approach to joint transmitter adaptation and power control in wireless systems.

PubMed

Popescu, Dimitrie C; Rawat, Danda B; Popescu, Otilia; Saquib, Mohamad

2010-06-01

Game theory has emerged as a new mathematical tool in the analysis and design of wireless communication systems, being particularly useful in studying the interactions among adaptive transmitters that attempt to achieve specific objectives without cooperation. In this paper, we present a game-theoretic approach to the problem of joint transmitter adaptation and power control in wireless systems, where users' transmissions are subject to quality-of-service requirements specified in terms of target signal-to-interference-plus-noise ratios (SINRs) and nonideal vector channels between transmitters and receivers are explicitly considered. Our approach is based on application of separable games, which are a specific class of noncooperative games where the players' cost is a separable function of their strategic choices. We formally state a joint codeword and power adaptation game, which is separable, and we study its properties in terms of its subgames, namely, the codeword adaptation subgame and the power adaptation subgame. We investigate the necessary conditions for an optimal Nash equilibrium and show that this corresponds to an ensemble of user codewords and powers, which maximizes the sum capacity of the corresponding multiaccess vector channel model, and for which the specified target SINRs are achieved with minimum transmitted power.

4D Dynamic Required Navigation Performance Final Report

NASA Technical Reports Server (NTRS)

Finkelsztein, Daniel M.; Sturdy, James L.; Alaverdi, Omeed; Hochwarth, Joachim K.

2011-01-01

New advanced four dimensional trajectory (4DT) procedures under consideration for the Next Generation Air Transportation System (NextGen) require an aircraft to precisely navigate relative to a moving reference such as another aircraft. Examples are Self-Separation for enroute operations and Interval Management for in-trail and merging operations. The current construct of Required Navigation Performance (RNP), defined for fixed-reference-frame navigation, is not sufficiently specified to be applicable to defining performance levels of such air-to-air procedures. An extension of RNP to air-to-air navigation would enable these advanced procedures to be implemented with a specified level of performance. The objective of this research effort was to propose new 4D Dynamic RNP constructs that account for the dynamic spatial and temporal nature of Interval Management and Self-Separation, develop mathematical models of the Dynamic RNP constructs, "Required Self-Separation Performance" and "Required Interval Management Performance," and to analyze the performance characteristics of these air-to-air procedures using the newly developed models. This final report summarizes the activities led by Raytheon, in collaboration with GE Aviation and SAIC, and presents the results from this research effort to expand the RNP concept to a dynamic 4D frame of reference.

40 CFR 98.398 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... or delivered as undifferentiated product. Natural Gas Liquids (NGLs) for the purposes of reporting under this subpart means hydrocarbons that are separated from natural gas as liquids through the process... GREENHOUSE GAS REPORTING Suppliers of Petroleum Products § 98.398 Definitions. Except as specified in this...

Compositions and methods for making selenocysteine containing polypeptides

DOEpatents

Soll, Dieter; Aldag, Caroline; Hohn, Michael

2016-10-11

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

49 CFR 572.81 - General description.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) ANTHROPOMORPHIC TEST DEVICES 9-Month Old Child § 572.81 General description. (a) The dummy consists of: (1) The assembly specified in drawing LP 1049/A, March 1979, which is described in its entirety by means of approximately 54 separate drawings and...

48 CFR 16.601 - Time-and-materials contracts.

Code of Federal Regulations, 2010 CFR

2010-10-01

... awarded without adequate price competition (see 15.403-1(c)(1)), the contract shall specify separate fixed...-Commercial Item Acquisitions With Adequate Price Competition, in solicitations contemplating use of a Time... based on adequate price competition. If authorized by agency procedures, the contracting officer may...

Background-Source Cosmic-Photon Elevation Scaling and Cosmic-Neutron/Photon Date Scaling in MCNP6

NASA Astrophysics Data System (ADS)

Tutt, J.; Anderson, C.; McKinney, G.

Cosmic neutron and photon fluxes are known to scale exponentially with elevation. Consequently, cosmic neutron elevation scaling was implemented for use with the background-source option shortly after its introduction into MCNP6, whereby the neutron flux weight factor was adjusted by the elevation scaling factor when the user-specified elevation differed from the selected background.dat grid-point elevation. At the same time, an elevation scaling factor was suggested for the cosmic photon flux, however, cosmic photon elevation scaling is complicated by the fact that the photon background consists of two components: cosmic and terrestrial. Previous versions of the background.dat file did not provide any way to separate these components. With Rel. 4 of this file in 2015, two new columns were added that provide the energy grid and differential cosmic photon flux separately from the total photon flux. Here we show that the cosmic photon flux component can now be scaled independently and combined with the terrestrial component to form the total photon flux at a user-specified elevation in MCNP6. Cosmic background fluxes also scale with the solar cycle due to solar modulation. This modulation has been shown to be nearly sinusoidal over time, with an inverse effect - increased modulation leads to a decrease in cosmic fluxes. This effect was initially included with the cosmic source option in MCNP6 and has now been extended for use with the background source option when: (1) the date is specified in the background.dat file, and (2) when the user specifies a date on the source definition card. A description of the cosmic-neutron/photon date scaling feature will be presented along with scaling results for past and future date extrapolations.

Gas separation by composite solvent-swollen membranes

DOEpatents

Matson, S.L.; Lee, E.K.L.; Friesen, D.T.; Kelly, D.J.

1989-04-25

There is disclosed a composite immobilized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorus or sulfur atom, and having a boiling point of at least 100 C and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation. 3 figs.

Gas separation by composite solvent-swollen membranes

DOEpatents

Matson, Stephen L.; Lee, Eric K. L.; Friesen, Dwayne T.; Kelly, Donald J.

1989-01-01

There is disclosed a composite immobulized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorous or sulfur atom, and having a boiling point of at least 100.degree. C. and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation.

Issues on the diagnosis and etiopathogenesis of mood disorders: reconsidering DSM-5.

PubMed

Ogasawara, Kazuyoshi; Nakamura, Yukako; Kimura, Hiroyuki; Aleksic, Branko; Ozaki, Norio

2018-02-01

The authors present a narrative review from the diagnostic and nosologic viewpoints of mood disorders (bipolar and depressive ones) by revisiting the revision from the fourth edition of the Diagnostic and Statistical Manual of Mental Disorders, Text Revision to DSM-5, including the following: the separation of the bipolar and depressive sections; the addition of increased energy and continuation of symptoms to the hypo/manic criteria; the elimination of mixed episodes; the creation of new categories and specifiers ("other specified bipolar and related disorder", "disruptive mood dysregulation disorder", "with anxious distress", "with mixed features", "with peripartum onset"); the categorization of hypo/manic episodes during antidepressant treatment into bipolar disorder; the elimination of the "bereavement exclusion"; the ambiguous separation between bipolar I and II; the insufficient distinction between "other specified bipolar and related disorders" and major depressive disorder; the differentiation regarding borderline personality disorder; agitation; premenstrual dysphoric disorder; and society and psychiatry. Through this analysis, we point out both the achievements and limitations of DSM-5. In addition, to examine the future direction of psychiatry, we introduce our cohort study regarding maternal depression and an outline of the National Institute of Mental Health's Research Domain Criteria project in the US. Finally, we advocate the importance of elucidating etiopathogeneses by starting from or going beyond the DSM operational diagnostic system, which has shown great efficacy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Unseren, M.A.

A general framework for solving the dynamic load distribution when two manipulators hold a rigid object is proposed. The underspecified problem of solving for the contact forces and torques based on the object`s equations of motion is transformed into a well specified problem. This is accomplished by augmenting the object`s equations of motion with additional equations which relate a new vector variable quantifying the internal contact force and torque degrees of freedom (DOF) as a linear function of the contact forces and torques. The resulting augmented system yields a well specified solution for the contact forces and torques in whichmore » they are separated into their motion inducing and internal components. A particular solution is suggested which enables the designer to conveniently specify what portion of the payload`s mass each manipulator is to bear. It is also shown that the results of the previous work are just a special case of the general load distribution framework described here.« less

40 CFR 179.24 - Ex parte discussions; separation of functions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... hearing, or by the Administrator, depending on who received the communication. An oral communication... hearing, who is involved in an oral communication contrary to this section, must, to the extent necessary... oral communication contrary to this section will be permitted. (d) The prohibitions specified in...

17 CFR 33.7 - Disclosure.

Code of Federal Regulations, 2014 CFR

2014-04-01

... option customer, other than for a customer specified in § 1.55(f) of this chapter, unless the futures commission merchant or introducing broker first: (i) Furnishes the option customer with a separate written... includes either such statement in a booklet containing the customer account agreement and other disclosure...

17 CFR 33.7 - Disclosure.

Code of Federal Regulations, 2013 CFR

2013-04-01

... option customer, other than for a customer specified in § 1.55(f) of this chapter, unless the futures commission merchant or introducing broker first: (i) Furnishes the option customer with a separate written... includes either such statement in a booklet containing the customer account agreement and other disclosure...

Modifications modulate anticodon loop dynamics and codon recognition of E. coli tRNA(Arg1,2).

PubMed

Cantara, William A; Bilbille, Yann; Kim, Jia; Kaiser, Rob; Leszczyńska, Grażyna; Malkiewicz, Andrzej; Agris, Paul F

2012-03-02

Three of six arginine codons are read by two tRNA(Arg) isoacceptors in Escherichia coli. The anticodon stem and loop of these isoacceptors (ASL(Arg1,2)) differs only in that the position 32 cytidine of tRNA(Arg1) is posttranscriptionally modified to 2-thiocytidine (s(2)C(32)). The tRNA(Arg1,2) are also modified at positions 34 (inosine, I(34)) and 37 (2-methyladenosine, m(2)A(37)). To investigate the roles of modifications in the structure and function, we analyzed six ASL(Arg1,2) constructs differing in their array of modifications by spectroscopy and codon binding assays. Thermal denaturation and circular dichroism spectroscopy indicated that modifications contribute thermodynamic and base stacking properties, resulting in more order but less stability. NMR-derived structures of the ASL(Arg1,2) showed that the solution structures of the ASLs were nearly identical. Surprisingly, none possessed the U-turn conformation required for effective codon binding on the ribosome. Yet, all ASL(Arg1,2) constructs efficiently bound the cognate CGU codon. Three ASLs with I(34) were able to decode CGC, whereas only the singly modified ASL(Arg1,2)(ICG) with I(34) was able to decode CGA. The dissociation constants for all codon bindings were physiologically relevant (0.4-1.4 μM). However, with the introduction of s(2)C(32) or m(2)A(37) to ASL(Arg1,2)(ICG), the maximum amount of ASL bound to CGU and CGC was significantly reduced. These results suggest that, by allowing loop flexibility, the modifications modulate the conformation of the ASL(Arg1,2), which takes one structure free in solution and two others when bound to the cognate arginyl-tRNA synthetase or to codons on the ribosome where modifications reduce or restrict binding to specific codons. Copyright © 2011 Elsevier Ltd. All rights reserved.

Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast

PubMed Central

Han, Lu; Kon, Yoshiko

2015-01-01

The numerous modifications of tRNA play central roles in controlling tRNA structure and translation. Modifications in and around the anticodon loop often have critical roles in decoding mRNA and in maintaining its reading frame. Residues U38 and U39 in the anticodon stem–loop are frequently modified to pseudouridine (Ψ) by members of the widely conserved TruA/Pus3 family of pseudouridylases. We investigate here the cause of the temperature sensitivity of pus3Δ mutants of the yeast Saccharomyces cerevisiae and find that, although Ψ38 or Ψ39 is found on at least 19 characterized cytoplasmic tRNA species, the temperature sensitivity is primarily due to poor function of tRNAGln(UUG), which normally has Ψ38. Further investigation reveals that at elevated temperatures there are substantially reduced levels of the s2U moiety of mcm5s2U34 of tRNAGln(UUG) and the other two cytoplasmic species with mcm5s2U34, that the reduced s2U levels occur in the parent strain BY4741 and in the widely used strain W303, and that reduced levels of the s2U moiety are detectable in BY4741 at temperatures as low as 33°C. Additional examination of the role of Ψ38,39 provides evidence that Ψ38 is important for function of tRNAGln(UUG) at permissive temperature, and indicates that Ψ39 is important for the function of tRNATrp(CCA) in trm10Δ pus3Δ mutants and of tRNALeu(CAA) as a UAG nonsense suppressor. These results provide evidence for important roles of both Ψ38 and Ψ39 in specific tRNAs, and establish that modification of the wobble position is subject to change under relatively mild growth conditions. PMID:25505024

Evaluating Sense Codon Reassignment with a Simple Fluorescence Screen.

PubMed

Biddle, Wil; Schmitt, Margaret A; Fisk, John D

2015-12-22

Understanding the interactions that drive the fidelity of the genetic code and the limits to which modifications can be made without breaking the translational system has practical implications for understanding the molecular mechanisms of evolution as well as expanding the set of encodable amino acids, particularly those with chemistries not provided by Nature. Because 61 sense codons encode 20 amino acids, reassigning the meaning of sense codons provides an avenue for biosynthetic modification of proteins, furthering both fundamental and applied biochemical research. We developed a simple screen that exploits the absolute requirement for fluorescence of an active site tyrosine in green fluorescent protein (GFP) to probe the pliability of the degeneracy of the genetic code. Our screen monitors the restoration of the fluorophore of GFP by incorporation of a tyrosine in response to a sense codon typically assigned another meaning in the genetic code. We evaluated sense codon reassignment at four of the 21 sense codons read through wobble interactions in Escherichia coli using the Methanocaldococcus jannaschii orthogonal tRNA/aminoacyl tRNA synthetase pair originally developed and commonly used for amber stop codon suppression. By changing only the anticodon of the orthogonal tRNA, we achieved sense codon reassignment efficiencies between 1% (Phe UUU) and 6% (Lys AAG). Each of the orthogonal tRNAs preferentially decoded the codon traditionally read via a wobble interaction in E. coli with the exception of the orthogonal tRNA with an AUG anticodon, which incorporated tyrosine in response to both the His CAU and His CAC codons with approximately equal frequencies. We applied our screen in a high-throughput manner to evaluate a 10(9)-member combined tRNA/aminoacyl tRNA synthetase library to identify improved sense codon reassigning variants for the Lys AAG codon. A single rapid screen with the ability to broadly evaluate reassignable codons will facilitate identification and improvement of the combinations of sense codons and orthogonal pairs that display efficient reassignment.

Metrics for More than Two Points at Once

NASA Technical Reports Server (NTRS)

Wolpert, David H.

2005-01-01

The conventional definition of a topological metric over a space specifies properties that must be obeyed by any measure of "how separated" two points in that space are. Here it is shown how to extend that definition, and in particular the triangle inequality, to concern arbitrary numbers of points. Such a measure of how separated the points within a collection are can be bootstrapped, to measure "how separated" from each other are two (or more) collections. The measure presented here also allows fractional membership of an element in a collection. This means it directly concerns measures of "how spread out" a probability distribution over a space is. When such a measure is bootstrapped to compare two collections, it allows us to measure how separated two probability distributions are, or more generally, how separated a distribution of distributions is.

40 CFR 60.482-1a - Standards: General.

Code of Federal Regulations, 2014 CFR

2014-07-01

... time during the specified monitoring period (e.g., month, quarter, year), provided the monitoring is... Monthly Quarterly Semiannually. (2) Pumps and valves that are shared among two or more batch process units... be separated by at least 120 calendar days. (g) If the storage vessel is shared with multiple process...

40 CFR 60.482-1a - Standards: General.

Code of Federal Regulations, 2012 CFR

2012-07-01

... time during the specified monitoring period (e.g., month, quarter, year), provided the monitoring is... Monthly Quarterly Semiannually. (2) Pumps and valves that are shared among two or more batch process units... be separated by at least 120 calendar days. (g) If the storage vessel is shared with multiple process...

40 CFR 60.482-1a - Standards: General.

Code of Federal Regulations, 2010 CFR

2010-07-01

... time during the specified monitoring period (e.g., month, quarter, year), provided the monitoring is... Monthly Quarterly Semiannually. (2) Pumps and valves that are shared among two or more batch process units... be separated by at least 120 calendar days. (g) If the storage vessel is shared with multiple process...

40 CFR 60.482-1a - Standards: General.

Code of Federal Regulations, 2013 CFR

2013-07-01

... time during the specified monitoring period (e.g., month, quarter, year), provided the monitoring is... Monthly Quarterly Semiannually. (2) Pumps and valves that are shared among two or more batch process units... be separated by at least 120 calendar days. (g) If the storage vessel is shared with multiple process...

40 CFR 60.482-1a - Standards: General.

Code of Federal Regulations, 2011 CFR

2011-07-01

... time during the specified monitoring period (e.g., month, quarter, year), provided the monitoring is... Monthly Quarterly Semiannually. (2) Pumps and valves that are shared among two or more batch process units... be separated by at least 120 calendar days. (g) If the storage vessel is shared with multiple process...

40 CFR 89.108 - Adjustable parameters, requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... this subpart. (d) For engines that use noncommercial fuels significantly different than the specified test fuel of the same type, the manufacturer may ask to use the parameter-adjustment provisions of 40... separate engine family. See 40 CFR 1039.801 for the definition of “noncommercial fuels”. [59 FR 31335, June...

40 CFR 89.108 - Adjustable parameters, requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... this subpart. (d) For engines that use noncommercial fuels significantly different than the specified test fuel of the same type, the manufacturer may ask to use the parameter-adjustment provisions of 40... separate engine family. See 40 CFR 1039.801 for the definition of “noncommercial fuels”. [59 FR 31335, June...

40 CFR 89.108 - Adjustable parameters, requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... this subpart. (d) For engines that use noncommercial fuels significantly different than the specified test fuel of the same type, the manufacturer may ask to use the parameter-adjustment provisions of 40... separate engine family. See 40 CFR 1039.801 for the definition of “noncommercial fuels”. [59 FR 31335, June...

40 CFR 89.108 - Adjustable parameters, requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... this subpart. (d) For engines that use noncommercial fuels significantly different than the specified test fuel of the same type, the manufacturer may ask to use the parameter-adjustment provisions of 40... separate engine family. See 40 CFR 1039.801 for the definition of “noncommercial fuels”. [59 FR 31335, June...

40 CFR 89.108 - Adjustable parameters, requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... this subpart. (d) For engines that use noncommercial fuels significantly different than the specified test fuel of the same type, the manufacturer may ask to use the parameter-adjustment provisions of 40... separate engine family. See 40 CFR 1039.801 for the definition of “noncommercial fuels”. [59 FR 31335, June...

29 CFR 1910.110 - Storage and handling of liquefied petroleum gases.

Code of Federal Regulations, 2012 CFR

2012-07-01

... dehydrators or dryers. (13) Ventilation, adequate—when specified for the prevention of fire during normal..., buildings, or separate fire divisions of buildings used exclusively for housing internal combustion engines..., diaphragms, etc., shall be of such quality as to be resistant to the action of liquefied petroleum gas under...

29 CFR 1910.110 - Storage and handling of liquefied petroleum gases.

Code of Federal Regulations, 2014 CFR

2014-07-01

... dehydrators or dryers. (13) Ventilation, adequate—when specified for the prevention of fire during normal..., buildings, or separate fire divisions of buildings used exclusively for housing internal combustion engines..., diaphragms, etc., shall be of such quality as to be resistant to the action of liquefied petroleum gas under...

29 CFR 1910.110 - Storage and handling of liquefied petroleum gases.

Code of Federal Regulations, 2013 CFR

2013-07-01

... dehydrators or dryers. (13) Ventilation, adequate—when specified for the prevention of fire during normal..., buildings, or separate fire divisions of buildings used exclusively for housing internal combustion engines..., diaphragms, etc., shall be of such quality as to be resistant to the action of liquefied petroleum gas under...

49 CFR 571.218 - Standard No. 218; Motorcycle helmets.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 6 2012-10-01 2012-10-01 false Standard No. 218; Motorcycle helmets. 571.218... Motor Vehicle Safety Standards § 571.218 Standard No. 218; Motorcycle helmets. Link to an amendment... retention system or its components shall attain the loads specified without separation; and (b) The...

49 CFR 571.218 - Standard No. 218; Motorcycle helmets.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 6 2011-10-01 2011-10-01 false Standard No. 218; Motorcycle helmets. 571.218... Motor Vehicle Safety Standards § 571.218 Standard No. 218; Motorcycle helmets. Link to an amendment... retention system or its components shall attain the loads specified without separation; and (b) The...

NPDES Permit for Buckley Air Force Base Municipal Separate Storm Sewer System in Colorado

EPA Pesticide Factsheets

Under NPDES permit CO-R042003, the U.S. Air Force is authorized to discharge from all MS4 outfalls existing as of the effective date of this permit to specified receiving waters within the exterior boundaries of Buckley Air Force Base, in Aurora, Colorado

5 CFR 550.1401 - Purpose.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Compensatory Time Off for Travel § 550.1401 Purpose. This subpart contains OPM regulations implementing 5 U.S.C. 5550b, which establishes a separate type of compensatory time off. Subject to the conditions specified... for time in a travel status away from the employee's official duty station when the travel time is not...

5 CFR 550.1401 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Compensatory Time Off for Travel § 550.1401 Purpose. This subpart contains OPM regulations implementing 5 U.S.C. 5550b, which establishes a separate type of compensatory time off. Subject to the conditions specified... for time in a travel status away from the employee's official duty station when the travel time is not...

5 CFR 550.1401 - Purpose.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Compensatory Time Off for Travel § 550.1401 Purpose. This subpart contains OPM regulations implementing 5 U.S.C. 5550b, which establishes a separate type of compensatory time off. Subject to the conditions specified... for time in a travel status away from the employee's official duty station when the travel time is not...

5 CFR 550.1401 - Purpose.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Compensatory Time Off for Travel § 550.1401 Purpose. This subpart contains OPM regulations implementing 5 U.S.C. 5550b, which establishes a separate type of compensatory time off. Subject to the conditions specified... for time in a travel status away from the employee's official duty station when the travel time is not...

5 CFR 550.1401 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Compensatory Time Off for Travel § 550.1401 Purpose. This subpart contains OPM regulations implementing 5 U.S.C. 5550b, which establishes a separate type of compensatory time off. Subject to the conditions specified... for time in a travel status away from the employee's official duty station when the travel time is not...

40 CFR 1042.135 - Labeling.

Code of Federal Regulations, 2011 CFR

2011-07-01

... label. (e) For engines requiring ULSD, create a separate label with the statement: “ULTRA LOW SULFUR... power (in kW), and power density (in kW/L) as needed to determine the emission standards for the engine family. You may specify displacement, maximum engine power, or power density as a range consistent with...

Children's Inferential Comprehension of Pragmatic Causal Relations in Reading.

ERIC Educational Resources Information Center

Morgan, Argiro Louchis

A study investigated the separate and combined effects of the syntactic organization of the sentence, the contextual framework in which a message is embedded, and the readers' past experiences on children's inferential reading comprehension of pragmatic cause/effect statements. The subjects, 144 fourth grade students, were asked to specify the…

40 CFR 721.7720 - Poly(oxy-1,2-ethanediyl), α,α′-[(1-methylethylidene) di-4,1-phenylene] bis [ω-(oxiranyl-methoxy)-.

Code of Federal Regulations, 2011 CFR

2011-07-01

...)(ii): Oil and grease separation. (b) Specific requirements. The provisions of subpart A of this part...), (b)(2), (c)(1), and (c)(2). (v) Release to water. Requirements as specified in § 721.90 (a)(2)(ii...

40 CFR 721.7720 - Poly(oxy-1,2-ethanediyl), α,α′-[(1-methylethylidene) di-4,1-phenylene] bis [ω-(oxiranyl-methoxy)-.

Code of Federal Regulations, 2010 CFR

2010-07-01

...)(ii): Oil and grease separation. (b) Specific requirements. The provisions of subpart A of this part...), (b)(2), (c)(1), and (c)(2). (v) Release to water. Requirements as specified in § 721.90 (a)(2)(ii...

48 CFR 22.407 - Solicitation provision and contract clauses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Adjustment (None or Separately Specified Pricing Method), in solicitations and contracts if the contract is... determines the most appropriate contract price adjustment method is the method at 22.404-12(c)(1) or (2); or....222-31, Davis-Bacon Act—Price Adjustment (Percentage Method), in solicitations and contracts if the...

40 CFR 160.43 - Test system care facilities.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (1) In tests with plants or aquatic animals, proper separation of species can be accomplished within..., aquarium, or housing unit. (2) Aquatic toxicity tests for individual projects shall be isolated to the... protocol. (h) For plants, an adequate supply of soil of the appropriate composition, as specified in the...

The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

PubMed

Komar, Anton A

2016-01-01

Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion

PubMed Central

O’Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U.; Ling, Jiqiang; Odoi, Keturah; Liu, Wenshe R.; Söll, Dieter

2012-01-01

Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to ‘statistical protein’ that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNAPyl orthogonal pair cannot completely outcompete contamination by natural amino acids. PMID:23036644

Structure of the MazF-mt9 toxin, a tRNA-specific endonuclease from Mycobacterium tuberculosis.

PubMed

Chen, Ran; Tu, Jie; Liu, Zhihui; Meng, Fanrong; Ma, Pinyun; Ding, Zhishan; Yang, Chengwen; Chen, Lei; Deng, Xiangyu; Xie, Wei

2017-05-06

Tuberculosis (TB) is a severe disease caused by Mycobacterium tuberculosis (M. tb) and the well-characterized M. tb MazE/F proteins play important roles in stress adaptation. Recently, the MazF-mt9 toxin has been found to display endonuclease activities towards tRNAs but the mechanism is unknown. We hereby present the crystal structure of apo-MazF-mt9. The enzyme recognizes tRNA Lys with a central UUU motif within the anticodon loop, but is insensitive to the sequence context outside of the loop. Based on our crystallographic and biochemical studies, we identified key residues for catalysis and proposed the potential tRNA-binding site. Copyright © 2017 Elsevier Inc. All rights reserved.

The concept of a plasma centrifuge with a high frequency rotating magnetic field and axial circulation

NASA Astrophysics Data System (ADS)

Borisevich, V. D.; Potanin, E. P.

2017-07-01

The possibility of using a rotating magnetic field (RMF) in a plasma centrifuge (PC), with axial circulation to multiply the radial separation effect in an axial direction, is considered. For the first time, a traveling magnetic field (TMF) is proposed to drive an axial circulation flow in a PC. The longitudinal separation effect is calculated for a notional model, using specified operational parameters and the properties of a plasma, comprising an isotopic mixture of 20Ne-22Ne and generated by a high frequency discharge. The optimal intensity of a circulation flow, in which the longitudinal separation effect reaches its maximum value, is studied. The optimal parameters of the RMF and TMF for effective separation, as well as the centrifuge performance, are calculated.

40 CFR 60.482-1 - Standards: General.

Code of Federal Regulations, 2011 CFR

2011-07-01

... operations. An owner or operator may monitor at any time during the specified monitoring period (e.g., month... shared among two or more batch process units that are subject to this subpart may be monitored at the... conducted annually, monitoring events must be separated by at least 120 calendar days. (g) If the storage...

40 CFR 60.482-1 - Standards: General.

Code of Federal Regulations, 2012 CFR

2012-07-01

... operations. An owner or operator may monitor at any time during the specified monitoring period (e.g., month... shared among two or more batch process units that are subject to this subpart may be monitored at the... conducted annually, monitoring events must be separated by at least 120 calendar days. (g) If the storage...

40 CFR 60.482-1 - Standards: General.

Code of Federal Regulations, 2013 CFR

2013-07-01

... operations. An owner or operator may monitor at any time during the specified monitoring period (e.g., month... shared among two or more batch process units that are subject to this subpart may be monitored at the... conducted annually, monitoring events must be separated by at least 120 calendar days. (g) If the storage...

40 CFR 60.482-1 - Standards: General.

Code of Federal Regulations, 2014 CFR

2014-07-01

... operations. An owner or operator may monitor at any time during the specified monitoring period (e.g., month... are shared among two or more batch process units that are subject to this subpart may be monitored at... conducted annually, monitoring events must be separated by at least 120 calendar days. (g) If the storage...

40 CFR 60.482-1 - Standards: General.

Code of Federal Regulations, 2010 CFR

2010-07-01

... operations. An owner or operator may monitor at any time during the specified monitoring period (e.g., month... shared among two or more batch process units that are subject to this subpart may be monitored at the... conducted annually, monitoring events must be separated by at least 120 calendar days. (g) If the storage...

42 CFR 435.201 - Individuals included in optional groups.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 4 2014-10-01 2014-10-01 false Individuals included in optional groups. 435.201... optional groups. (a) The agency may choose to cover as optional categorically needy any group or groups of... eligibility criteria for groups specified in the separate sections of this subpart: (1) Aged individuals (65...

48 CFR 852.236-83 - Payments under fixed-price construction contracts (including NAS).

Code of Federal Regulations, 2011 CFR

2011-10-01

... (CPM) network. (4) The CPM network shall include a separate cost loaded activity for adjusting and... (cold, constant temperature) 5 Entire air-conditioning system (Specified under 600 Sections) 5 Entire... equipment as are approved by the resident engineer for storage will be included. (3) Such materials and/or...

40 CFR 60.1090 - What must I do with my revised materials separation plan?

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) STANDARDS OF PERFORMANCE FOR NEW STATIONARY SOURCES Standards of Performance for Small Municipal Waste Combustion Units for Which Construction is Commenced After August 30... must do two tasks: (a) As specified under “Reporting” (§ 60.1375), submit five items to the...

42 CFR 409.87 - Blood deductible.

Code of Federal Regulations, 2010 CFR

2010-10-01

... after plasma is separated from whole blood. (2) A unit of packed red cells is treated as the equivalent... red cells—(1) Basic rule. Except as specified in paragraph (b)(2) of this section, the beneficiary is... hospital's or CAH's charges for the blood or packed red cells or arranging for it to be replaced. (2...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN”) may be applied in place of the symbol;; (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN”) may be applied in place of the symbol;; (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN” may be applied in place of the symbol); (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN” may be applied in place of the symbol); (2) A packaging identification code designating the type...

Microprocessor-Based Neural-Pulse-Wave Analyzer

NASA Technical Reports Server (NTRS)

Kojima, G. K.; Bracchi, F.

1983-01-01

Microprocessor-based system analyzes amplitudes and rise times of neural waveforms. Displaying histograms of measured parameters helps researchers determine how many nerves contribute to signal and specify waveform characteristics of each. Results are improved noise rejection, full or partial separation of overlapping peaks, and isolation and identification of related peaks in different histograms. 2

Can We Separate Verbs from Their Argument Structure? A Group Study in Aphasia

ERIC Educational Resources Information Center

Caley, Sarah; Whitworth, Anne; Claessen, Mary

2017-01-01

Background: Given the integral role that verbs play in sentence production, understanding verb deficits is critical to clinical practice. Difficulties in sentence production are often directly related to an inability to retrieve argument structure information which, according to most theoretical accounts, is specified at a lexical level as part of…

27 CFR 555.218 - Table of distances for storage of explosive materials.

Code of Federal Regulations, 2010 CFR

2010-04-01

... with traffic volume of more than 3,000 vehicles/day Barricaded Unbarricaded Separation of magazines... explosive materials are defined in § 555.11. (2) When two or more storage magazines are located on the same property, each magazine must comply with the minimum distances specified from inhabited buildings, railways...

38 CFR 9.1 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the policy. (g) The term termination of duty means (1) In the case of active duty or active duty for training being performed under a call or order that does not specify a period of less than 31 days-discharge, release or separation from such duty. (2) In the case of other duty—the member's release from his...

38 CFR 9.1 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the policy. (g) The term termination of duty means (1) In the case of active duty or active duty for training being performed under a call or order that does not specify a period of less than 31 days-discharge, release or separation from such duty. (2) In the case of other duty—the member's release from his...

30 CFR 285.521 - Do my financial assurance requirements change as activities progress on my limited lease or grant?

Code of Federal Regulations, 2010 CFR

2010-07-01

... separate decommissioning bond or other financial assurance instrument must meet the requirements specified... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Do my financial assurance requirements change... EXISTING FACILITIES ON THE OUTER CONTINENTAL SHELF Payments and Financial Assurance Requirements Financial...

40 CFR 63.1579 - What definitions apply to this subpart?

Code of Federal Regulations, 2014 CFR

2014-07-01

... regeneration of catalyst in situ in any one of several reactors (e.g., 4 or 5 separate reactors) that can be..., wet injection, or caustic injection control device that treats (in-situ) the catalytic reforming unit...) at specified intervals or at the owner's or operator's convenience for in situ catalyst regeneration...

40 CFR 63.1579 - What definitions apply to this subpart?

Code of Federal Regulations, 2013 CFR

2013-07-01

... regeneration of catalyst in situ in any one of several reactors (e.g., 4 or 5 separate reactors) that can be..., wet injection, or caustic injection control device that treats (in-situ) the catalytic reforming unit...) at specified intervals or at the owner's or operator's convenience for in situ catalyst regeneration...

40 CFR 63.1579 - What definitions apply to this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

... regeneration of catalyst in situ in any one of several reactors (e.g., 4 or 5 separate reactors) that can be..., wet injection, or caustic injection control device that treats (in-situ) the catalytic reforming unit...) at specified intervals or at the owner's or operator's convenience for in situ catalyst regeneration...

40 CFR 1033.112 - Emission diagnostics for SCR systems.

Code of Federal Regulations, 2012 CFR

2012-07-01

... diagnostic system must monitor reductant quality and tank levels and alert operators to the need to refill... specified in § 1033.110 and an audible alarm. You do not need to separately monitor reductant quality if you include an exhaust NOX sensor (or other sensor) that allows you to determine inadequate reductant quality...

40 CFR 1033.112 - Emission diagnostics for SCR systems.

Code of Federal Regulations, 2014 CFR

2014-07-01

... diagnostic system must monitor reductant quality and tank levels and alert operators to the need to refill... specified in § 1033.110 and an audible alarm. You do not need to separately monitor reductant quality if you include an exhaust NOX sensor (or other sensor) that allows you to determine inadequate reductant quality...

40 CFR 1033.112 - Emission diagnostics for SCR systems.

Code of Federal Regulations, 2011 CFR

2011-07-01

... diagnostic system must monitor reductant quality and tank levels and alert operators to the need to refill... specified in § 1033.110 and an audible alarm. You do not need to separately monitor reductant quality if you include an exhaust NOX sensor (or other sensor) that allows you to determine inadequate reductant quality...

Background-Source Cosmic-Photon Elevation Scaling and Cosmic-Neutron/Photon Date Scaling in MCNP6

DOE PAGES

Tutt, James Robert; Anderson, Casey Alan; McKinney, Gregg Walter

2017-10-26

Here, cosmic neutron and photon fluxes are known to scale exponentially with elevation. Consequently, cosmic neutron elevation scaling was implemented for use with the background-source option shortly after its introduction into MCNP6, whereby the neutron flux weight factor was adjusted by the elevation scaling factor when the user-specified elevation differed from the selected background.dat grid-point elevation. At the same time, an elevation scaling factor was suggested for the cosmic photon flux, however, cosmic photon elevation scaling is complicated by the fact that the photon background consists of two components: cosmic and terrestrial. Previous versions of the background.dat file did notmore » provide any way to separate these components. With Rel. 4 of this file in 2015, two new columns were added that provide the energy grid and differential cosmic photon flux separately from the total photon flux. Here we show that the cosmic photon flux component can now be scaled independently and combined with the terrestrial component to form the total photon flux at a user-specified elevation in MCNP6.« less

Background-Source Cosmic-Photon Elevation Scaling and Cosmic-Neutron/Photon Date Scaling in MCNP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tutt, James Robert; Anderson, Casey Alan; McKinney, Gregg Walter

Here, cosmic neutron and photon fluxes are known to scale exponentially with elevation. Consequently, cosmic neutron elevation scaling was implemented for use with the background-source option shortly after its introduction into MCNP6, whereby the neutron flux weight factor was adjusted by the elevation scaling factor when the user-specified elevation differed from the selected background.dat grid-point elevation. At the same time, an elevation scaling factor was suggested for the cosmic photon flux, however, cosmic photon elevation scaling is complicated by the fact that the photon background consists of two components: cosmic and terrestrial. Previous versions of the background.dat file did notmore » provide any way to separate these components. With Rel. 4 of this file in 2015, two new columns were added that provide the energy grid and differential cosmic photon flux separately from the total photon flux. Here we show that the cosmic photon flux component can now be scaled independently and combined with the terrestrial component to form the total photon flux at a user-specified elevation in MCNP6.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnette, Daniel W.

eCo-PylotDB, written completely in Python, provides a script that parses incoming emails and prepares extracted data for submission to a database table. The script extracts the database server, the database table, the server password, and the server username all from the email address to which the email is sent. The database table is specified on the Subject line. Any text in the body of the email is extracted as user comments for the database table. Attached files are extracted as data files with each file submitted to a specified table field but in separate rows of the targeted database table.more » Other information such as sender, date, time, and machine from which the email was sent is extracted and submitted to the database table as well. An email is sent back to the user specifying whether the data from the initial email was accepted or rejected by the database server. If rejected, the return email includes details as to why.« less

7 CFR 301.85 - Quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Soil, compost, humus, muck, peat, and decomposed manure, separately or with other things. (2) Plants with roots, except soil-free aquatic plants. (3) Grass sod. (4) Plant crowns and roots for propagation... measurement by a sizing screen or sizing chain, each is substantially free of soil as a result of grading (a...

7 CFR 301.85 - Quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Soil, compost, humus, muck, peat, and decomposed manure, separately or with other things. (2) Plants with roots, except soil-free aquatic plants. (3) Grass sod. (4) Plant crowns and roots for propagation... measurement by a sizing screen or sizing chain, each is substantially free of soil as a result of grading (a...

7 CFR 301.85 - Quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Soil, compost, humus, muck, peat, and decomposed manure, separately or with other things. (2) Plants with roots, except soil-free aquatic plants. (3) Grass sod. (4) Plant crowns and roots for propagation... measurement by a sizing screen or sizing chain, each is substantially free of soil as a result of grading (a...

7 CFR 301.85 - Quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Soil, compost, humus, muck, peat, and decomposed manure, separately or with other things. (2) Plants with roots, except soil-free aquatic plants. (3) Grass sod. (4) Plant crowns and roots for propagation... measurement by a sizing screen or sizing chain, each is substantially free of soil as a result of grading (a...

7 CFR 301.85 - Quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Soil, compost, humus, muck, peat, and decomposed manure, separately or with other things. (2) Plants with roots, except soil-free aquatic plants. (3) Grass sod. (4) Plant crowns and roots for propagation... measurement by a sizing screen or sizing chain, each is substantially free of soil as a result of grading (a...

14 CFR 17.27 - Submission of joint or separate statements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... either— (1) A joint request for ADR, and an executed ADR agreement, pursuant to § 17.33(d), specifying which ADR techniques will be employed; or (2) Written explanation(s) as to why ADR proceedings will not... Register. (d) The submission of a statement which indicates that ADR will not be utilized will not in any...

14 CFR 17.27 - Submission of joint or separate statements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... either— (1) A joint request for ADR, and an executed ADR agreement, pursuant to § 17.33(d), specifying which ADR techniques will be employed; or (2) Written explanation(s) as to why ADR proceedings will not... Register. (d) The submission of a statement which indicates that ADR will not be utilized will not in any...

The Role of Collegiality in Higher Education Tenure, Promotion, and Termination Decisions.

ERIC Educational Resources Information Center

Connell, Mary Ann; Savage, Frederick G.

2001-01-01

Presents an analysis of the arguments for and against consideration of collegiality in higher education employment decisions and a review of the relevant case law. Critics argue that unless collegiality is specified as a separate criterion for evaluation in the faculty contract or handbook, its use is a breach of contract. Others are concerned…

77 FR 33733 - Regulation of Fuel and Fuel Additives: Modification to Octamix Waiver (TXCeed)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-07

... must meet ASTM volatility specifications contained in ASTM D439-85a, as well as phase separation conditions specified in ASTM D-2 Proposal P-176 and Texas Methanol alcohol purity specifications. \\4\\ 53 FR..., TXCeed, met ASTM \\11\\ and NACE \\12\\ corrosion test results, as well as physical property information. \\11...

48 CFR 22.404-12 - Labor standards for contracts containing construction requirements and option provisions that...

Code of Federal Regulations, 2010 CFR

2010-10-01

... contract price as a result of the incorporation of a new or revised wage determination at the exercise of... contracting officer may include in the contract a separately specified pricing method that permits an... term of the contract. At the time of option exercise, the contracting officer must incorporate a new...

76 FR 58155 - Defense Federal Acquisition Regulation Supplement; Construction and Architect-Engineer Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-20

... past performance for construction and Architect- Engineer services. On April 19, 2011, DoD published a... electronically collecting past performance data; there is no need to specify separate DoD forms to collect the... this rule other than the cost of internet access should small entities choose to comment on their past...

Public Interest Waiver of American Iron and Steel Requirements to the Winston-Salem and Forsyth County City/County Utilities Commission for 30 Inch TR Flex Pipe Fittings

EPA Pesticide Factsheets

Product specific project waivers apply only to the specified product and proposed project referenced in the waiver. Any other project that wishes to use a similar product must apply for a separate waiver based on specific project circumstances.

10 CFR 70.38 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Conduct a radiation survey of the premises where the licensed activities were carried out and submit a... becquerels (picocuries) per gram for solids such as soils or concrete; and (ii) Specify the survey instrument... this section; or (2) The licensee has decided to permanently cease principal activities, as defined in...

48 CFR 52.222-30 - Davis-Bacon Act-Price Adjustment (None or Separately Specified Method).

Code of Federal Regulations, 2010 CFR

2010-10-01

... for elsewhere in this contract, to cover any increases or decreases in wages and benefits as a result of— (1) Incorporation of the Department of Labor's wage determination applicable at the exercise of... applied to the contract by operation of law; or (3) An increase in wages and benefits resulting from any...

The Inauguration of the Child Development Film Archives. Final Report.

ERIC Educational Resources Information Center

Popplestone, John A.; McPherson, Marion White

The cataloging of films acquired by the Child Development Film Archives disclosed approximately 3500 separate units, or 804,232 feet of footage. An inventory sheet has been completed for each film which provides a record of the content of each cinema, and collectively, constitute a table of contents to the total collection. Variables specified on…

40 CFR 63.5993 - What performance tests and other procedures must I use?

Code of Federal Regulations, 2010 CFR

2010-07-01

... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Rubber Tire Manufacturing General... specified in § 63.7(e)(1). (d) You must conduct three separate test runs for each performance test required... test run must last at least 1 hour. (e) If you are complying with the emission limitations using a...

Differential Language Markers of Pathology in Autism, Pervasive Developmental Disorder Not Otherwise Specified and Specific Language Impairment

ERIC Educational Resources Information Center

Demouy, Julie; Plaza, Monique; Xavier, Jean; Ringeval, Fabien; Chetouani, Mohamed; Perisse, Didier; Chauvin, Dominique; Viaux, Sylvie; Golse, Bernard; Cohen, David; Robel, Laurence

2011-01-01

Language impairment is a common core feature in Pervasive Developmental Disorders (PDD) and Specific Language Impairment (SLI). Many studies have tried to define the specific language profiles of these disorders, some claiming the existence of overlaps, and others conceiving of them as separate categories. Fewer have sought to determine whether…

48 CFR 852.246-75 - Warranty for construction-guarantee period services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... comply with the contract, terminate the right to proceed with the work (or the separable part of the work... complete the work within this specified time, whether or not the contractor's right to proceed with the... contractor fail to prosecute the work or fail to proceed promptly to provide guarantee period services after...

Polyphonic Music Information Retrieval Based on Multi-Label Cascade Classification System

ERIC Educational Resources Information Center

Jiang, Wenxin

2009-01-01

Recognition and separation of sounds played by various instruments is very useful in labeling audio files with semantic information. This is a non-trivial task requiring sound analysis, but the results can aid automatic indexing and browsing music data when searching for melodies played by user specified instruments. Melody match based on pitch…

Control of vortical separation on conical bodies

NASA Technical Reports Server (NTRS)

Mourtos, Nikos J.; Roberts, Leonard

1987-01-01

In a variety of aeronautical applications, the flow around conical bodies at incidence is of interest. Such applications include, but are not limited to, highly maneuverable aircraft with delta wings, the aerospace plane and nose portions of spike inlets. The theoretical model used has three parts. First, the single line vortex model is used within the framework of slender body theory, to compute the outer inviscid field for specified separation lines. Next, the three dimensional boundary layer is represented by a momentum equation for the cross flow, analogous to that for a plane boundary layer; a von Karman Pohlhausen approximation is applied to solve this equation. The cross flow separation for both laminar and turbulent layers is determined by matching the pressure at the upper and lower separation points. This iterative procedure yields a unique solution for the separation lines and consequently for the position of the vortices and the vortex lift on the body. Lastly, control of separation is achieved by blowing tangentially from a slot located along a cone generator. It is found that for very small blowing coefficients, the separation can be postponed or suppressedy completely.

Leigh syndrome caused by a novel m.4296G>A mutation in mitochondrial tRNA isoleucine.

PubMed

Cox, Rachel; Platt, Julia; Chen, Li Chieh; Tang, Sha; Wong, Lee-Jun; Enns, Gregory M

2012-03-01

Leigh syndrome is a severe neurodegenerative disease with heterogeneous genetic etiology. We report a novel m.4296G>A variant in the mitochondrial tRNA isoleucine gene in a child with Leigh syndrome, mitochondrial proliferation, lactic acidosis, and abnormal respiratory chain enzymology. The variant is present at >75% heteroplasmy in blood and cultured fibroblasts from the proband, <5% in asymptomatic maternal relatives, and is absent in 3000 controls. It is located in the highly conserved anticodon region of tRNA(Ile) where three other pathogenic changes have been described. We conclude that there is strong evidence to classify m.4296G>A as a pathogenic mutation causing Leigh syndrome. Copyright © 2011 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Preliminary feasibility study of pallet-only mode for magnetospheric and plasmas in space payloads, volume 4

NASA Technical Reports Server (NTRS)

1976-01-01

Results of studies performed on the magnetospheric and plasma portion of the AMPS are presented. Magnetospheric and plasma in space experiments and instruments are described along with packaging (palletization) concepts. The described magnetospheric and plasma experiments were considered as separate entities. Instrumentation ospheric and plasma experiments were considered as separate entities. Instrumentation requirements and operations were formulated to provide sufficient data for unambiguous interpretation of results without relying upon other experiments of the series. Where ground observations are specified, an assumption was made that large-scale additions or modifications to existing facilities were not required.

[An influence of mental disorder in the child on the parents in the context of differentiated approaches to psychosocial interventions on childhood psychiatry].

PubMed

Koren E V; Kupriyanova, T A; Dubinskaya, A O; Khairetdinov, O Z

2014-01-01

To specify parent reaction to a mental disorder in the child and to develop differential approaches to psychosocial family interventions. Authors studied parents (mostly mothers) of 140 children with schizophrenia spectrum disorders, 100 children with autistic disorders and 85 children with mental retardation. Along with psychiatric examination of the parents, it was used psychometric scales ECI and CGSQ. Authors specified emotional and behavioral characteristics of the parents' reaction as common for all diseases studied as well peculiar for separated forms of mental diseases in children. The factors (cognitive, emotional and behavioral) determining the targets of differentiated therapeutic interventions were singled out. The stress coping strategies for parents are formulated.

MESH2D Grid generator design and use

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flach, G. P.

Mesh2d is a Fortran90 program originally designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). x-coordinates depending only on index i implies strictly vertical x-grid lines, whereas the y-grid lines can undulate. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations. Since the original development effort, Mesh2d has been extended to more general two-dimensional structured grids of the form [x(i,j),(i,j)].

Role of a texture gradient in the perception of relative size.

PubMed

Tozawa, Junko

2010-01-01

Two theories regarding the role of a texture gradient in the perception of the relative size of objects are compared. Relational theory states that relative size is directly specified by the projective ratio of the numbers of texture elements spanned by objects. Distance calibration theory assumes that relative size is a product of visual angle and distance, once the distance is specified by the texture. Experiment 1 involved three variables: background (no texture, texture gradient patterns), the ratio of heights of the comparison stimulus to a standard (three levels), and angular vertical separation of the standard stimulus below the horizon (two levels). The effect of the retinal length of the comparison stimulus was examined in experiment 2. In both experiments, participants judged both the apparent size and distance of a comparison stimulus relative to a standard stimulus. Results suggest that the cues selected by observers to judge relative size were to some degree different from those used to judge relative distance. Relative size was strongly affected by a texture gradient and the retinal length of a comparison stimulus whereas relative distance perception was affected by relative height. When dominant cues that specify size are different from those which specify distance, relational theory might provide a better account of relative size perception than distance calibration theory.

17 CFR 270.19a-1 - Written statement to accompany dividend payments by management companies.

Code of Federal Regulations, 2010 CFR

2010-04-01

... that an open-end company may treat as a separate source its net profits from such sales during its... specify the sources from which the remainder was paid. Every company which in any fiscal year elects to... dividend payments by management companies. 270.19a-1 Section 270.19a-1 Commodity and Securities Exchanges...

40 CFR 80.1453 - What are the product transfer document (PTD) requirements for the RFS program?

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (8) The RIN status (Assigned or Separated). (9) The RIN generation year. (10) The associated reason... paragraphs (a)(1) through (a)(10) of this section. (B) The identifying information for a RIN that is transferred in EMTS uniquely is the information specified in paragraphs (a)(1) through (a)(10) of this section...

40 CFR 80.1453 - What are the product transfer document (PTD) requirements for the RFS program?

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (8) The RIN status (Assigned or Separated). (9) The RIN generation year. (10) The associated reason... paragraphs (a)(1) through (a)(10) of this section. (B) The identifying information for a RIN that is transferred in EMTS uniquely is the information specified in paragraphs (a)(1) through (a)(10) of this section...

40 CFR 80.615 - What penalties apply under this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... specified in section 205 of the Clean Air Act (42 U.S.C. 7524) for every day of each such violation and the... and every day the non-complying diesel fuel remains any place in the distribution system. (2) Any... subject to a separate day of violation for each and every day that the noncomplying fuel remains any place...

40 CFR 80.405 - What penalties apply under this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... subject to civil penalties as specified in section 205 of the Clean Air Act for every day of each such... violation for each and every day in the averaging period. Any person liable under § 80.395(b) for a failure... correction, is subject to a separate day of violation for each and every day in the averaging period in which...

75 FR 57659 - Airworthiness Directives Eurocopter France (ECF) Model SA-365N1, AS-365N2, AS 365 N3, EC 155B...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-22

... aviation authority of the European Aviation Safety Agency (EASA). The MCAI AD reports the separation and...: DOT/FAA Southwest Region, Gary Roach, ASW-111, Aviation Safety Engineer, Rotorcraft Directorate... Rulemaking Title 49 of the United States Code specifies the FAA's authority to issue rules on aviation safety...

Arts and Cultural Education at School in Europe. Germany 2007/08

ERIC Educational Resources Information Center

Lohmar, Brigitte

2008-01-01

The Ministry of Education of the land (regional level) is responsible for setting the specified aims for the cultural and creative dimensions of education. The ministry decides also about the creation and the implementation of the arts curriculum. The arts curriculum at ISCED levels 1 and 2 (age group: 6-15/16) is organised as separate subjects.…

36 CFR 1238.30 - What must agencies do when transferring permanent microform records to the National Archives of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... specified in § 1232.14(c) of this subchapter. (c) Transfer the silver gelatin original (or duplicate silver gelatin microform created in accordance with § 1238.14) plus one microform copy. (d) Ensure that the... separately from the silver gelatin original or silver duplicate microform copy and clearly label them as non...

Simulation techniques for estimating error in the classification of normal patterns

NASA Technical Reports Server (NTRS)

Whitsitt, S. J.; Landgrebe, D. A.

1974-01-01

Methods of efficiently generating and classifying samples with specified multivariate normal distributions were discussed. Conservative confidence tables for sample sizes are given for selective sampling. Simulation results are compared with classified training data. Techniques for comparing error and separability measure for two normal patterns are investigated and used to display the relationship between the error and the Chernoff bound.

36 CFR 1238.30 - What must agencies do when transferring permanent microform records to the National Archives of...

Code of Federal Regulations, 2011 CFR

2011-07-01

... specified in § 1232.14(c) of this subchapter. (c) Transfer the silver gelatin original (or duplicate silver gelatin microform created in accordance with § 1238.14) plus one microform copy. (d) Ensure that the... separately from the silver gelatin original or silver duplicate microform copy and clearly label them as non...

36 CFR 1238.30 - What must agencies do when transferring permanent microform records to the National Archives of...

Code of Federal Regulations, 2014 CFR

2014-07-01

... specified in § 1232.14(c) of this subchapter. (c) Transfer the silver gelatin original (or duplicate silver gelatin microform created in accordance with § 1238.14) plus one microform copy. (d) Ensure that the... separately from the silver gelatin original or silver duplicate microform copy and clearly label them as non...

36 CFR 1238.30 - What must agencies do when transferring permanent microform records to the National Archives of...

Code of Federal Regulations, 2012 CFR

2012-07-01

... specified in § 1232.14(c) of this subchapter. (c) Transfer the silver gelatin original (or duplicate silver gelatin microform created in accordance with § 1238.14) plus one microform copy. (d) Ensure that the... separately from the silver gelatin original or silver duplicate microform copy and clearly label them as non...

36 CFR § 1238.30 - What must agencies do when transferring permanent microform records to the National Archives of...

Code of Federal Regulations, 2013 CFR

2013-07-01

... information specified in § 1232.14(c) of this subchapter. (c) Transfer the silver gelatin original (or duplicate silver gelatin microform created in accordance with § 1238.14) plus one microform copy. (d) Ensure... non-silver copies separately from the silver gelatin original or silver duplicate microform copy and...

Summary of a Competency Based, Field Centered, Systems Approach to Elementary Teacher Education. Summary of the Final Report.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

A competency-based, field-centered systems approach to elementary school teacher education was designed to bring about specified, measurable outcomes, to have evidence of its effectiveness continually available, and to be adaptive in the light of that evidence. The model was separated into two interdependent parts, the instructional model and the…

40 CFR 721.7780 - Poly[oxy(methyl-1,2-ethane-diyl)], α,α′-(2,2-dimethyl-1,3-pro-pan-ediyl)bis[ω-(oxi-rany-me-thoxy)-.

Code of Federal Regulations, 2011 CFR

2011-07-01

... technologies in § 721.90(a)(2)(ii): Oil and grease separation. (b) Specific requirements. The provisions of.... Requirements as specified in § 721.85 (b)(1), (b)(2), (c)(1), and (c)(2). (v) Release to water. Requirements as...

21 CFR 133.102 - Asiago fresh and asiago soft cheese.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of this section, the word “milk” means cow's milk, which may be adjusted by separating part of the..., asiago soft cheese, is the food prepared from milk and other ingredients specified in this section, by... § 133.5 (a), (b), and (d). It is cured for not less than 60 days. (b) Milk which may be pasteurized or...

26 CFR 1.682(a)-1 - Income of trust in case of divorce, etc.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 8 2012-04-01 2012-04-01 false Income of trust in case of divorce, etc. 1.682(a... case of divorce, etc. (a) In general. (1) Section 682(a) provides rules in certain cases for... specified to be for the support of the obligor spouse's minor children in the divorce or separate...

26 CFR 1.682(a)-1 - Income of trust in case of divorce, etc.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Income of trust in case of divorce, etc. 1.682(a... case of divorce, etc. (a) In general. (1) Section 682(a) provides rules in certain cases for... specified to be for the support of the obligor spouse's minor children in the divorce or separate...

26 CFR 1.682(a)-1 - Income of trust in case of divorce, etc.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 8 2014-04-01 2014-04-01 false Income of trust in case of divorce, etc. 1.682(a... case of divorce, etc. (a) In general. (1) Section 682(a) provides rules in certain cases for... specified to be for the support of the obligor spouse's minor children in the divorce or separate...

26 CFR 1.682(a)-1 - Income of trust in case of divorce, etc.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Income of trust in case of divorce, etc. 1.682(a... case of divorce, etc. (a) In general. (1) Section 682(a) provides rules in certain cases for... specified to be for the support of the obligor spouse's minor children in the divorce or separate...

77 FR 5990 - Special Conditions: Learjet Inc., Model LJ-200-1A10 Airplane, Pilot-Compartment View Through...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-07

... airflow to maintain a clear-vision area. The heavy rain and high speed conditions specified in the current... to maintain a sufficiently clear area of the windshield in low-speed flight or during surface... airflow disturbance or separation on the windshield could cause failure to maintain a clear-vision area on...

Flight Experiment Investigation of General Aviation Self-Separation and Sequencing Tasks

NASA Technical Reports Server (NTRS)

Murdoch, Jennifer L.; Ramiscal, Ermin R.; McNabb, Jennifer L.; Bussink, Frank J. L.

2005-01-01

A new flight operations concept called Small Aircraft Transportation System (SATS) Higher Volume Operations (HVO) was developed to increase capacity during Instrument Meteorological Conditions (IMC) at non-towered, non-radar airports by enabling concurrent operations of multiple aircraft. One aspect of this concept involves having pilots safely self-separate from other aircraft during approaches into these airports using appropriate SATS HVO procedures. A flight experiment was conducted to determine if instrument-rated general aviation (GA) pilots could self-separate and sequence their ownship aircraft, while following a simulated aircraft, into a non-towered, non-radar airport during simulated IMC. Six GA pilots' workload levels and abilities to perform self-separation and sequencing procedures while flying a global positioning system (GPS) instrument approach procedure were examined. The results showed that the evaluation pilots maintained at least the minimum specified separation between their ownship aircraft and simulated traffic and maintained their assigned landing sequence 100-percent of the time. Neither flight path deviations nor subjective workload assessments were negatively impacted by the additional tasks of self-separating and sequencing during these instrument approaches.

A simple method for the analysis of particle sizes of forage and total mixed rations.

PubMed

Lammers, B P; Buckmaster, D R; Heinrichs, A J

1996-05-01

A simple separator was developed to determine the particle sizes of forage and TMR that allows for easy separation of wet forage into three fractions and also allows plotting of the particle size distribution. The device was designed to mimic the laboratory-scale separator for forage particle sizes that was specified by Standard S424 of the American Society of Agricultural Engineers. A comparison of results using the standard device and the newly developed separator indicated no difference in ability to predict fractions of particles with maximum length of less than 8 and 19 mm. The separator requires a small quantity of sample (1.4 L) and is manually operated. The materials on the screens and bottom pan were weighed to obtain the cumulative percentage of sample that was undersize for the two fractions. The results were then plotted using the Weibull distribution, which proved to be the best fit for the data. Convenience samples of haycrop silage, corn silage, and TMR from farms in the northeastern US were analyzed using the forage and TMR separator, and the range of observed values are given.

Computing Q-D Relationships for Storage of Rocket Fuels

NASA Technical Reports Server (NTRS)

Jester, Keith

2005-01-01

The Quantity Distance Measurement Tool is a GIS BASEP computer program that aids safety engineers by calculating quantity-distance (Q-D) relationships for vessels that contain explosive chemicals used in testing rocket engines. (Q-D relationships are standard relationships between specified quantities of specified explosive materials and minimum distances by which they must be separated from persons, objects, and other explosives to obtain specified types and degrees of protection.) The program uses customized geographic-information-system (GIS) software and calculates Q-D relationships in accordance with NASA's Safety Standard For Explosives, Propellants, and Pyrotechnics. Displays generated by the program enable the identification of hazards, showing the relationships of propellant-storage-vessel safety buffers to inhabited facilities and public roads. Current Q-D information is calculated and maintained in graphical form for all vessels that contain propellants or other chemicals, the explosiveness of which is expressed in TNT equivalents [amounts of trinitrotoluene (TNT) having equivalent explosive effects]. The program is useful in the acquisition, siting, construction, and/or modification of storage vessels and other facilities in the development of an improved test-facility safety program.

Simulation and analysis of a geopotential research mission

NASA Technical Reports Server (NTRS)

White, Lisa K.

1987-01-01

Methods for the determination of the initial conditions for the two satellites that will satisfy Geopotential Research Mission (GRM) requirements are investigated. For certain gravitational recovery techniques, the satellites must remain close to a specified separation distance and their groundtracks must repeat after a specified interval of time. Since the objective of the GRM mission is to improve the gravity model, any pre-mission orbit predicted using existing gravity models will be in error. A technique has been developed to eliminate the drift between the two satellites caused by gravitational modeling errors and return them to repeating groundtracks. The concept of frozen orbits, which minimize altitude variations over given latitudes, was investigated. Finally, the effects of temporal perturbations on the relative range-rate signal were studied. At the proposed altitude of 160 km, the range-rate signal produced by perturbations other than the static geopotential field are dominated by the luni-solar effect. This study demonstrates that the combined effects of all the temporal perturbations does not prevent the orbit from being frozen or the satellites from obtaining a repeating groundtrack to within a specified closure distance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogle, James M.; Brodersen, Ditlev E.; Clemons, William M.

Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognatemore » tRNA. The third, or 'wobble,' position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.« less

Program for Research on Dietary Supplements in Military Operations and Healthcare Metabolically Optimized Brain - JWF

DTIC Science & Technology

2014-05-01

Alcohol; Vitamins / Minerals / Antioxidants / Dietary supplements (not specified); Herbal Medicine (Subsets: Ginseng and Gingko Biloba); Diet...looking specifically at the role of glucose (Hoyland 2008). c. Other Intervention Groupings considered: i. Herbal Medicine : 58 abstracts identified...involved herbal medicine (excluding gingko biloba and ginseng) as an intervention on the healthy adult population. 31 separate herb or herbal

40 CFR Appendix J to Part 50 - Reference Method for the Determination of Particulate Matter as PM10 in the Atmosphere

Code of Federal Regulations, 2014 CFR

2014-07-01

... size fraction in the PM1O size range is then collected on a separate filter over the specified sampling... Each filter is weighed (after moisture equilibration) before and after use to determine the net weight... of the mass concentration range is determined by the repeatability of filter tare weights, assuming...

40 CFR Appendix J to Part 50 - Reference Method for the Determination of Particulate Matter as PM10 in the Atmosphere

Code of Federal Regulations, 2012 CFR

2012-07-01

... size fraction in the PM1O size range is then collected on a separate filter over the specified sampling... Each filter is weighed (after moisture equilibration) before and after use to determine the net weight... of the mass concentration range is determined by the repeatability of filter tare weights, assuming...

40 CFR Appendix J to Part 50 - Reference Method for the Determination of Particulate Matter as PM10 in the Atmosphere

Code of Federal Regulations, 2013 CFR

2013-07-01

... size fraction in the PM1O size range is then collected on a separate filter over the specified sampling... Each filter is weighed (after moisture equilibration) before and after use to determine the net weight... of the mass concentration range is determined by the repeatability of filter tare weights, assuming...

40 CFR 721.5575 - Oxirane, 2,2′-(1,6-hex-ane-diyl-bis (oxymethylene)) bis-.

Code of Federal Regulations, 2011 CFR

2011-07-01

...)(1), and (c)(2). (v) Release to water. Requirements as specified in § 721.90 (a)(2)(ii), (b)(1), and (c)(1). The following may be used as an alternative to the technologies in § 721.90(a)(2)(ii): Oil and grease separation. (b) Specific requirements. The provisions of subpart A of this part apply to...

40 CFR 721.5575 - Oxirane, 2,2′-(1,6-hex-ane-diyl-bis (oxymethylene)) bis-.

Code of Federal Regulations, 2010 CFR

2010-07-01

...)(1), and (c)(2). (v) Release to water. Requirements as specified in § 721.90 (a)(2)(ii), (b)(1), and (c)(1). The following may be used as an alternative to the technologies in § 721.90(a)(2)(ii): Oil and grease separation. (b) Specific requirements. The provisions of subpart A of this part apply to...

Act No. 1183, Civil Code, 23 December 1985.

PubMed

1987-01-01

This document contains major provisions of Paraguay's 1985 Civil Code. The Code sets the marriage age at 16 for males and 14 for females and forbids marriage between natural and adopted relatives as well as between persons of the same sex. Bigamy is forbidden, as is marriage between a person and someone convicted of attempting or committing homicide against that person's spouse. Legal incompetents may not marry. Underage minors may marry with the permission of their parents or a court. Noted among the rights and duties of a married couple is the stipulation that husbands (or a judge) must give their approval before wives can legally run a business or work outside of the house or perform other specified activities. Valid marriages are dissolved only upon the death of one spouse. Remarriage in Paraguay after divorce abroad is forbidden. Spouses may legally separate after 2 years of married life (married minors must remain together until 2 years past the age of majority). Marital separation may be requested for adultery, attempted homicide by one spouse upon the other, dishonest or immoral conduct, extreme cruelty or abuse, voluntary or malicious abandonment, or the state of habitual intoxication or repeated use of drugs. Marriages can be annulled in specified cases. Marital property is subject to the community property regime, but each spouse may retain control of specified types of personal property. The Code appoints the husband as manager of community property within limits and reserves certain property to the wife. The Code permits premarital agreements about property management, and covers the dissolution and liquidation of the community property regime. The Code also sets provisions governing "de facto" unions; filiation for children born in and outside of wedlock; claims for parental recognition; kinship; and the duty to provide maintenance to spouses, children, and other relatives.

Selective Fluorination and Separation of Metals with NF3 for Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, Richard A.; Barinaga, Charles J.; McNamara, Bruce K.

2016-03-01

We report recent progress on the development of a new methodology based on the generation of volatile metal fluorides through the use of nitrogen trifluoride (NF3), and the separation and measurement of these metal fluorides by electron ionization mass spectrometry. Though unreactive under ambient conditions, NF3 reacts selectively at specified temperatures with various metal-containing species to form volatile metal fluorides. Utilizing these species-dependent traits, elements of a sample may be sequentially produced and thus separated on-line. Metals were reacted inside a thermogravimetric analyzer, the gas outlet of which was directly coupled to a quadrupole mass spectrometer with an electron impactmore » ionization source via a molecular leak valve. We present results of this project including the electron ionization mass spectrum of gaseous tellurium hexafluoride.« less

Analysis of crossover between local and massive separation on airfoils

NASA Technical Reports Server (NTRS)

Barnett, Mark

1987-01-01

The occurrence of massive separation on airfoils operating at high Reynolds number poses an important problem to the aerodynamicist. In the present study, the phenomenon of crossover, induced by airfoil thickness, between local separation and massive separation is investigated for low speed (incompressible), symmetric flow past realistic airfoil geometries. This problem is studied both for the infinite Reynolds number asymptotic limit using triple-deck theory and for finite Reynolds number using interacting boundary-layer theory. Numerical results are presented which illustrate how the flow evolves from local to massive separation as the airfoil thickness is increased. The results of the triple-deck and the interacting boundary-layer analyses are found to be in qualitative agreement for the NACA four digit series and an uncambered supercritical airfoil. The effect of turbulence on the evolution of the flow is also considered. Solutions are presented for turbulent flows past a NACA 0014 airfoil and a circular cylinder. For the latter case, the calculated surface pressure distribution is found to agree well with experimental data if the proper eddy pressure level is specified.

Joint Blind Source Separation by Multi-set Canonical Correlation Analysis

PubMed Central

Li, Yi-Ou; Adalı, Tülay; Wang, Wei; Calhoun, Vince D

2009-01-01

In this work, we introduce a simple and effective scheme to achieve joint blind source separation (BSS) of multiple datasets using multi-set canonical correlation analysis (M-CCA) [1]. We first propose a generative model of joint BSS based on the correlation of latent sources within and between datasets. We specify source separability conditions, and show that, when the conditions are satisfied, the group of corresponding sources from each dataset can be jointly extracted by M-CCA through maximization of correlation among the extracted sources. We compare source separation performance of the M-CCA scheme with other joint BSS methods and demonstrate the superior performance of the M-CCA scheme in achieving joint BSS for a large number of datasets, group of corresponding sources with heterogeneous correlation values, and complex-valued sources with circular and non-circular distributions. We apply M-CCA to analysis of functional magnetic resonance imaging (fMRI) data from multiple subjects and show its utility in estimating meaningful brain activations from a visuomotor task. PMID:20221319

Low speed airfoil design and analysis

NASA Technical Reports Server (NTRS)

Eppler, R.; Somers, D. M.

1979-01-01

A low speed airfoil design and analysis program was developed which contains several unique features. In the design mode, the velocity distribution is not specified for one but many different angles of attack. Several iteration options are included which allow the trailing edge angle to be specified while other parameters are iterated. For airfoil analysis, a panel method is available which uses third-order panels having parabolic vorticity distributions. The flow condition is satisfied at the end points of the panels. Both sharp and blunt trailing edges can be analyzed. The integral boundary layer method with its laminar separation bubble analog, empirical transition criterion, and precise turbulent boundary layer equations compares very favorably with other methods, both integral and finite difference. Comparisons with experiment for several airfoils over a very wide Reynolds number range are discussed. Applications to high lift airfoil design are also demonstrated.

Tornado and extreme wind design criteria for nuclear power plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

1973-12-01

Nuclear power plant design criteria for tornadoes and extreme winds are presented. Data, formulas, and procedures for determining maximum wind loading on structures and parts of structures are included. Extreme wind loading is applied to structures using methods and procedures consistent with ANSI Building Code A58.1- 1972. The design wind velocities specified generally exceed 100-year recurrent interval winds. Tornado wind loading is applied to structures using procedures paralleling those for extrene winds with additional criteria resulting from the atmospheric pressure change accompanying tornadoes and tornado missile inipact effects. Tornado loading for the 48 contiguous United States is specified for twomore » major zones separated by the Continental Divide. A cross reference listing items related to Atomic Energy Commission Safety Analysis Report format is provided. Development supporting tornado criteria is included. (auth)« less

Two-tiered design analysis of a radiator for a solar dynamic powered Stirling engine

NASA Technical Reports Server (NTRS)

Hainley, Donald C.

1989-01-01

Two separate design approaches for a pumped loop radiator used to transfer heat from the cold end of a solar dynamic powered Stirling engine are described. The first approach uses a standard method to determine radiator requirements to meet specified end of mission conditions. Trade-off studies conducted for the analysis are included. Justification of this concept within the specified parameters of the analysis is provided. The second design approach determines the life performance of the radiator/Stirling system. In this approach, the system performance was altered by reducing the radiator heat transfer area. Performance effects and equilibrium points were determined as radiator segments were removed. This simulates the effect of loss of radiator sections due to micro-meteoroid and space debris penetration. The two designs were compared on the basis of overall system requirements and goals.

Two-tiered design analysis of a radiator for a solar dynamic powered Stirling engine

NASA Technical Reports Server (NTRS)

Hainley, Donald C.

1989-01-01

Two separate design approaches for a pumped loop radiator used to transfer heat from the cold end of a solar dynamic powered Stirling engine are described. The first approach uses a standard method to determine radiator requirements to meet specified end of mission conditions. Trade-off studies conducted for the analysis are included. Justification of this concept within the specified parameters of the analysis is provided. The second design approach determines the life performance of the radiator/Stirling system. In this approach, the system performance was altered by reducing the radiator heat transfer area. Performance effects and equilibrium points were determined as radiator segments were removed. This simulates the effect of loss of radiator sections due to micro-meteoroid and space debris penetration. The two designs are compared on the basis of overall system requirements and goals.

MIUS wastewater technology evaluation

NASA Technical Reports Server (NTRS)

Poradek, J. C.

1976-01-01

A modular integrated utility system wastewater-treatment process is described. Research in the field of wastewater treatment is reviewed, treatment processes are specified and evaluated, and recommendations for system use are made. The treatment processes evaluated are in the broad categories of preparatory, primary, secondary, and tertiary treatment, physical-chemical processing, dissolved-solids removal, disinfection, sludge processing, and separate systems. Capital, operating, and maintenance costs are estimated, and extensive references are given.

Operational Site Selection for Unmanned Aircraft

DTIC Science & Technology

2011-06-01

eliminate unsuitable areas, the Op Site Selection process must first consider landcover , terrain, and specifications for one or more UAS platforms...areas, the OSS process must first consider landcover , terrain, and specifi- cations for one or more UAS platforms. To select the most optimal sites, the...by landcover , ERDC/CERL TR-11-16 2 soil type, slope, and aspect. The individual terrain units are pre- determined and delineated by a separate

75 FR 20931 - Airworthiness Directives; Eurocopter France (ECF) Model SA-365N1, AS-365N2, AS 365 N3, EC 155B...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

... Community. The MCAI AD reports the separation and loss of a stainless steel ring (75 millimeter (mm) in... of a stainless steel ring (75 mm in diameter) from a blade sleeve resulting in severe, high-frequency... information specifies checking the blade sleeve for slippage of the stainless steel ring (75 mm in diameter...

Bifurcation Analysis of 1D Steady States of the Bénard Problem in the Long Wavelength Limit

NASA Astrophysics Data System (ADS)

Zhou, Chengzhe; Troian, Sandra

2015-11-01

We investigate the character and stability of stationary states of the (1 + 1) D evolution equation ∂t h +h3hxxx +h2∂x γ x = 0 describing the motion of an interface h (x , t) separating a thin warm viscous film from a thin cool inviscid layer where γ = γ (h) represents the interfacial tension. The phase diagram corresponding to all positive periodic steady states (PPSS) is specified by two variables - the global extrema of the equilibrum shape and a generalized mechanical interface pressure. The analytic forms describing the PPSS shapes, the minimal period, the average height and the generalized free energy are all confirmed numerically. We find there is at most one non-trivial PPSS for specified period and volume. We also find no stable perturbed PPSS near the critical point for volume conserving perturbations of identical period. A weakly non-linear analysis about the critical point yields bifurcations of the pitchfork-type. For all non-trivial PPSS, we verify the unstable nature of the PPSS by transforming the non-normal operator (resulting from the spatially inhomogeneous PPSS) to normal form, which we then solve by finite element computations.

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

PubMed Central

Wong, J. Tze-Fei; Ng, Siu-Kin; Mat, Wai-Kin; Hu, Taobo; Xue, Hong

2016-01-01

The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets. PMID:26999216

A-to-I RNA editing independent of ADARs in filamentous fungi

PubMed Central

Wang, Chenfang; Xu, Jin-Rong; Liu, Huiquan

2016-01-01

ABSTRACT ADAR mediated A-to-I RNA editing is thought to be unique to animals and occurs mainly in the non-coding regions. Recently filamentous fungi such as Fusarium graminearum were found to lack orthologs of animal ADARs but have stage-specific A-to-I editing during sexual reproduction. Unlike animals, majority of editing sites are in the coding regions and often result in missense and stop loss changes in fungi. Furthermore, whereas As in RNA stems are targeted by animal ADARs, RNA editing in fungi preferentially targets As in hairpin loops, implying that fungal RNA editing involves mechanisms related to editing of the anticodon loop by ADATs. Identification and characterization of fungal adenosine deaminases and their stage-specific co-factors may be helpful to understand the evolution of human ADARs. Fungi also can be used to study biological functions of missense and stop loss RNA editing events in eukaryotic organisms. PMID:27533598

Selection of the simplest RNA that binds isoleucine

PubMed Central

LOZUPONE, CATHERINE; CHANGAYIL, SHANKAR; MAJERFELD, IRENE; YARUS, MICHAEL

2003-01-01

We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA–amino acid binding structures. PMID:14561881

Frameshift Suppression in SACCHAROMYCES CEREVISIAE. V. Isolation and Genetic Properties of Nongroup-Specific Suppressors

PubMed Central

Culbertson, Michael R.; Gaber, Richard F.; Cummins, Claudia M.

1982-01-01

Two classes of frameshift suppressors distributed at 22 different loci were identified in previous studies in the yeast Saccharomyces cerevisiae. These suppressors exhibited allele-specific suppression of +1 G:C insertion mutations in either glycine or proline codons, designated as group II and group III frameshift mutations, respectively. Genes corresponding to representative suppressors of each group have been shown to encode altered glycine or proline tRNAs containing four base anticodons.—This communication reports the existence of a third class of frameshift suppressor that exhibits a wider range in specificity of suppression. The suppressors map at three loci, suf12, suf13, and suf14, which are located on chromosomes IV, XV, and XIV, respectively. The phenotypes of these suppressors suggest that suppression may be mediated by genes other than those encoding the primary structure of glycine or proline tRNAs. PMID:6757053

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

FlexibleSUSY-A spectrum generator generator for supersymmetric models

NASA Astrophysics Data System (ADS)

Athron, Peter; Park, Jae-hyeon; Stöckinger, Dominik; Voigt, Alexander

2015-05-01

We introduce FlexibleSUSY, a Mathematica and C++ package, which generates a fast, precise C++ spectrum generator for any SUSY model specified by the user. The generated code is designed with both speed and modularity in mind, making it easy to adapt and extend with new features. The model is specified by supplying the superpotential, gauge structure and particle content in a SARAH model file; specific boundary conditions e.g. at the GUT, weak or intermediate scales are defined in a separate FlexibleSUSY model file. From these model files, FlexibleSUSY generates C++ code for self-energies, tadpole corrections, renormalization group equations (RGEs) and electroweak symmetry breaking (EWSB) conditions and combines them with numerical routines for solving the RGEs and EWSB conditions simultaneously. The resulting spectrum generator is then able to solve for the spectrum of the model, including loop-corrected pole masses, consistent with user specified boundary conditions. The modular structure of the generated code allows for individual components to be replaced with an alternative if available. FlexibleSUSY has been carefully designed to grow as alternative solvers and calculators are added. Predefined models include the MSSM, NMSSM, E6SSM, USSM, R-symmetric models and models with right-handed neutrinos.

Conflict resolution maneuvers during near miss encounters with cockpit traffic displays

NASA Technical Reports Server (NTRS)

Palmer, E.

1983-01-01

The benefits and liabilities associated with pilots' use of a cockpit traffic display to assess the threat posed by air traffic and to make small maneuvers to avoid situations which would result in collision avoidance advisories are experimentally studied. The crew's task was to fly a simulated wide-body aircraft along a straight course at constant altitude while intruder aircraft appeared on a variety of converging trajectories. The main experimental variables were the amount and quality of the information displayed on the intruder aircraft's estimated future position. Pilots were to maintain a horizontal separation of at least 1.5 nautical miles or a vertical separation of 500 ft, so that collision avoidance advisories would not be triggered. The results show that pilots could usually maneuver to provide the specified separation but often made course deviations greater than 1.5 nm or 500 ft.

Disk MHD generator study

NASA Technical Reports Server (NTRS)

Retallick, F. D.

1980-01-01

Directly-fired, separately-fired, and oxygen-augmented MHD power plants incorporating a disk geometry for the MHD generator were studied. The base parameters defined for four near-optimum-performance MHD steam power systems of various types are presented. The finally selected systems consisted of (1) two directly fired cases, one at 1920 K (2996F) preheat and the other at 1650 K (2500 F) preheat, (2) a separately-fired case where the air is preheated to the same level as the higher temperature directly-fired cases, and (3) an oxygen augmented case with the same generator inlet temperature of 2839 (4650F) as the high temperature directly-fired and separately-fired cases. Supersonic Mach numbers at the generator inlet, gas inlet swirl, and constant Hall field operation were specified based on disk generator optimization. System pressures were based on optimization of MHD net power. Supercritical reheat stream plants were used in all cases. Open and closed cycle component costs are summarized and compared.

The phase topology of a special case of Goryachev integrability in rigid body dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryabov, P. E., E-mail: orelryabov@mail.ru

2014-07-31

The phase topology of a special case of Goryachev integrability in the problem of motion of a rigid body in a fluid is investigated using the method of Boolean functions, which was developed by Kharlamov for algebraically separated systems. The bifurcation diagram of the moment map is found and the Fomenko invariant, which classifies the systems up to rough Liouville equivalence, is specified. Bibliography: 15 titles. (paper)

A Study of Age Demographics across the Aviation and Missile Materiel Enterprise

DTIC Science & Technology

2016-03-31

Voluntary Separation Incentive Pay (VSIP) and Voluntary Early Retirement Authority ( VERA ) (Lytell, et al., 2015). History that Shaped the...MATERIEL ENTERPRISE DEMOGRAPHICS 10 skillsets or job series. The VERA , VSIP and retention allowances are tools that are most commonly used to help...control the desired “shape” of the workforce. VERA and VSIP are tools that shape the attrition rates and can be tailored towards specified series or

Turbo Pascal/GEM Software Interface for Scientific Graph Preparation

DTIC Science & Technology

1991-04-01

Well as whatever artistic touches that the author may desire. Even colour hardcopy reproduuction is possible through use of an appropriate colour...drawing axes on graphs. The unit also contains an autoscaling procedure that may be applied separately to all curve axes. 6.3.1 Available structures...procedures AxisScale Provides autoscaled values from specified min and max values. LabelRightAxis Draws ticks and numbers on the right axis. LabelXAxis

Principles and core functions of integrated child health information systems.

PubMed

Hinman, Alan R; Atkinson, Delton; Diehn, Tonya Norvell; Eichwald, John; Heberer, Jennifer; Hoyle, Therese; King, Pam; Kossack, Robert E; Williams, Donna C; Zimmerman, Amy

2004-11-01

Infants undergo a series of preventive and therapeutic health interventions and activities. Typically, each activity includes collection and submission of data to a dedicated information system. Subsequently, health care providers, families, and health programs must query each information system to determine the child's status in a given area. Efforts are underway to integrate information in these separate information systems. This requires specifying the core functions that integrated information systems must perform.

Equipment Development for Automatic Anthropometric Measurements

NASA Technical Reports Server (NTRS)

Cater, J. P.; Oakey, W. E.

1978-01-01

An automated procedure for measuring and recording the anthropometric active angles is presented. The small portable system consists of a microprocessor controlled video data acquisition system which measures single plane active angles using television video techniques and provides the measured data on sponsored-specified preformatted data sheets. This system, using only a single video camera, observes the end limits of the movement of a pair of separated lamps and calculates the vector angle between the extreme positions.

Incorporation of excess wild-type and mutant tRNA(3Lys) into human immunodeficiency virus type 1.

PubMed Central

Huang, Y; Mak, J; Cao, Q; Li, Z; Wainberg, M A; Kleiman, L

1994-01-01

Human immunodeficiency virus (HIV) particles produced in COS-7 cells transfected with HIV type 1 (HIV-1) proviral DNA contain 8 molecules of tRNA(3Lys) per 2 molecules of genomic RNA and 12 molecules of tRNA1,2Lys per 2 molecules of genomic RNA. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a human tRNA3Lys gene, there is a large increase in the amount of cytoplasmic tRNA3Lys per microgram of total cellular RNA, and the tRNA3Lys content in the virus increases from 8 to 17 molecules per 2 molecules of genomic RNA. However, the total number of tRNALys molecules per 2 molecules of genomic RNA remains constant at 20; i.e., the viral tRNA1,2Lys content decreases from 12 to 3 molecules per 2 molecules of genomic RNA. All detectable tRNA3Lys is aminoacylated in the cytoplasm of infected cells and deacylated in the virus. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a mutant amber suppressor tRNA3Lys gene (in which the anticodon is changed from TTT to CTA), there is also a large increase in the relative concentration of cytoplasmic tRNA3Lys, and the tRNA3Lys content in the virus increases from 8 to 15 molecules per 2 molecules of genomic RNA, with a decrease in viral tRNA1,2Lys from 12 to 5 molecules per 2 molecules of genomic RNA. Thus, the total number of molecules of tRNALys in the virion remains at 20. The alteration of the anticodon has little effect on the viral packaging of this mutant tRNA in spite of the fact that it no longer contains the modified base mcm 5s2U at position 34, and its ability to be aminoacylated is significantly impaired compared with that of wild-type tRNA3Lys. Viral particles which have incorporated either excess wild-type tRNA3Lys or mutant suppressor tRNA3Lys show no differences in viral infectivity compared with wild-type HIV-1. Images PMID:7966556

Reversible exciplex formation followed charge separation.

PubMed

Petrova, M V; Burshtein, A I

2008-12-25

The reversible exciplex formation followed by its decomposition into an ion pair is considered, taking into account the subsequent geminate and bulk ion recombination to the triplet and singlet products (in excited and ground states). The integral kinetic equations are derived for all state populations, assuming that the spin conversion is performed by the simplest incoherent (rate) mechanism. When the forward and backward electron transfer is in contact as well as all dissociation/association reactions of heavy particles, the kernels of integral equations are specified and expressed through numerous reaction constants and characteristics of encounter diffusion. The solutions of these equations are used to specify the quantum yields of the excited state and exciplex fluorescence induced by pulse or stationary pumping. In the former case, the yields of the free ions and triplet products are also found, while in the latter case their stationary concentrations are obtained.

A generalized predictive model for direct gain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Givoni, B.

In the correlational model for direct gain developed by the Los Alamos National Laboratory, a list of constants applicable to different types of buildings or passive solar systems was specified separately for each type. In its original form, the model was applicable only to buildings similar in their heat capacity, type of glazing, or night insulation to the types specified by the model. While maintaining the general form of the predictive equations, the new model, the predictive model for direct gain (PMDG), replaces the constants with functions dependent upon the thermal properties of the building, or the components of themore » solar system, or both. By this transformation, the LANL model for direct gain becomes a generalized one. The new model predicts the performance of buildings heated by direct gain with any heat capacity, glazing, and night insulation as functions of their thermophysical properties and climatic conditions.« less

Preloadable vector sensitive latch

NASA Technical Reports Server (NTRS)

Acres, William R. (Inventor)

1987-01-01

A preloadable vector-sensitive latch which automatically releases when the force vector from a latch memebr reaches a specified release angle is presented. In addition, it contains means to remove clearance between the latched members and to preload the latch to prevent separation at angles less than the specified release angle. The latch comprises a triangular main link, a free link connected between a first corner of the main link and a yoke member, a housing, and an actuator connected between the yoke member and the housing. A return spring bias means connects the main link to a portion of the housing. A second corner of the main link is slidably and pivotally connected to the housing via a slot in a web portion of the housing. The latch housing has a rigid docking ring alignable with a mating locking ring which is engageable by a locking roller journalled on the third corner of the triangular main link.

Methods of computing steady-state voltage stability margins of power systems

DOEpatents

Chow, Joe Hong; Ghiocel, Scott Gordon

2018-03-20

In steady-state voltage stability analysis, as load increases toward a maximum, conventional Newton-Raphson power flow Jacobian matrix becomes increasingly ill-conditioned so power flow fails to converge before reaching maximum loading. A method to directly eliminate this singularity reformulates the power flow problem by introducing an AQ bus with specified bus angle and reactive power consumption of a load bus. For steady-state voltage stability analysis, the angle separation between the swing bus and AQ bus can be varied to control power transfer to the load, rather than specifying the load power itself. For an AQ bus, the power flow formulation is only made up of a reactive power equation, thus reducing the size of the Jacobian matrix by one. This reduced Jacobian matrix is nonsingular at the critical voltage point, eliminating a major difficulty in voltage stability analysis for power system operations.

Research, development and demonstration of nickel-zinc batteries for electric vehicle propulsion

NASA Astrophysics Data System (ADS)

1980-06-01

The feasibility of the nickel zinc battery for electric vehicle propulsion is discussed. The program is divided into seven distinct but highly interactive tasks collectively aimed at the development and commercialization of nickel zinc technology. These basic technical tasks are separator development, electrode development, product design and analysis, cell/module battery testing, process development, pilot manufacturing, and thermal manufacturing, and thermal management. Significant progress has been made in the understanding of separator failure mechanisms, and a generic category of materials has been specified for the 300+ deep discharge applications. Shape change has been reduced significantly. Progress in the area of thermal management was significant, with the development of a model that accurately represents heat generation and rejection rates during battery operation.

Characterization of Glass Fiber Separator Material for Lithium Batteries

NASA Technical Reports Server (NTRS)

Subbarao, S.; Frank, H.

1984-01-01

Characterization studies were carried out on a glass fiber paper that is currently employed as a separator material for some LiSOCl2 primary cells. The material is of the non-woven type made from microfilaments of E-type glass and contains an ethyl acrylate binder. Results from extraction studies and tensile testing revealed that the binder content and tensile strength of the paper were significantly less than values specified by the manufacturer. Scanning electron micrographs revealed the presence of clusters of impurities many of which were high in iron content. Results of emission spectroscopy revealed high overall levels of iron and leaching, followed by atomic absorption measurements, revealed that essentially all of this iron is soluble in SOCl2.

MODFLOW-CDSS, a version of MODFLOW-2005 with modifications for Colorado Decision Support Systems

USGS Publications Warehouse

Banta, Edward R.

2011-01-01

MODFLOW-CDSS is a three-dimensional, finite-difference groundwater-flow model based on MODFLOW-2005, with two modifications. The first modification is the introduction of a Partition Stress Boundaries capability, which enables the user to partition a selected subset of MODFLOW's stress-boundary packages, with each partition defined by a separate input file. Volumetric water-budget components of each partition are tracked and listed separately in the volumetric water-budget tables. The second modification enables the user to specify that execution of a simulation should continue despite failure of the solver to satisfy convergence criteria. This modification is particularly intended to be used in conjunction with automated model-analysis software; its use is not recommended for other purposes.

Applicability of the iterative technique for cardiac resynchronization therapy optimization: full-disclosure, 50-sequential-patient dataset of transmitral Doppler traces, with implications for future research design and guidelines.

PubMed

Jones, Siana; Shun-Shin, Matthew J; Cole, Graham D; Sau, Arunashis; March, Katherine; Williams, Suzanne; Kyriacou, Andreas; Hughes, Alun D; Mayet, Jamil; Frenneaux, Michael; Manisty, Charlotte H; Whinnett, Zachary I; Francis, Darrel P

2014-04-01

Full-disclosure study describing Doppler patterns during iterative atrioventricular delay (AVD) optimization of biventricular pacemakers (cardiac resynchronization therapy, CRT). Doppler traces of the first 50 eligible patients undergoing iterative Doppler AVD optimization in the BRAVO trial were examined. Three experienced observers classified conformity to guideline-described patterns. Each observer then selected the optimum AVD on two separate occasions: blinded and unblinded to AVD. Four Doppler E-A patterns occurred: A (always merged, 18% of patients), B (incrementally less fusion at short AVDs, 12%), C (full separation at short AVDs, as described by the guidelines, 28%), and D (always separated, 42%). In Groups A and D (60%), the iterative guidelines therefore cannot specify one single AVD. On the kappa scale (0 = chance alone; 1 = perfect agreement), observer agreement for the ideal AVD in Classes B and C was poor (0.32) and appeared worse in Groups A and D (0.22). Blinding caused the scattering of the AVD selected as optimal to widen (standard deviation rising from 37 to 49 ms, P < 0.001). By blinding 28% of the selected optimum AVDs were ≤60 or ≥200 ms. All 50 Doppler datasets are presented, to support future methodological testing. In most patients, the iterative method does not clearly specify one AVD. In all the patients, agreement on the ideal AVD between skilled observers viewing identical images is poor. The iterative protocol may successfully exclude some extremely unsuitable AVDs, but so might simply accepting factory default. Irreproducibility of the gold standard also prevents alternative physiological optimization methods from being validated honestly.

Models for estimating runway landing capacity with Microwave Landing System (MLS)

NASA Technical Reports Server (NTRS)

Tosic, V.; Horonjeff, R.

1975-01-01

A model is developed which is capable of computing the ultimate landing runway capacity, under ILS and MLS conditions, when aircraft population characteristics and air traffic control separation rules are given. This model can be applied in situations when only a horizontal separation between aircraft approaching a runway is allowed, as well as when both vertical and horizontal separations are possible. It is assumed that the system is free of errors, that is that aircraft arrive at specified points along the prescribed flight path precisely when the controllers intend for them to arrive at these points. Although in the real world there is no such thing as an error-free system, the assumption is adequate for a qualitative comparison of MLS with ILS. Results suggest that an increase in runway landing capacity, caused by introducing the MLS multiple approach paths, is to be expected only when an aircraft population consists of aircraft with significantly differing approach speeds and particularly in situations when vertical separation can be applied. Vertical separation can only be applied if one of the types of aircraft in the mix has a very steep descent angle.

Development of a new seal for use on large openings of pressurized spacecraft

NASA Technical Reports Server (NTRS)

Weddendorf, B.

1994-01-01

The goal of this project was to design, build, and test an example of the seal invented by the author for use on Space Station Freedom and patented in 1991. The seal features a metallic spring core and replaceable elastomeric sealing elements. The metallic spring is designed to retain the sealing force of the elastomeric element against both sides of face seal gland for any specified amount of waviness or separation of the glands. A seal able to tolerate at least 1.3 mm (0.05 in) of flange distortion or separation and a test fixture of this seal which allowed direct comparison testing of O-rings were built. These designs were tested to compare leakage at different amounts of flange deflection. Results of the testing show the development seal exceeded its requirement to seal 1.3 mm of flange separation by 1 mm. This compared with the O-ring leakage, increasing dramatically at 0.5 mm of separation. The development seal also leaked at a lower rate than the O-ring seals in all tests.

Program Descriptions for Interactive Signal and Pattern Analysis and Recognition System (ISPARS).

DTIC Science & Technology

1984-03-01

procedures for the ISPARS components developed at the David Taylor Naval Ship Reserach and Development Center (DTNSRDC), which are not documented in other...an alphabetic character. Some commands may consist of a letter and one or two two-digit numbers, separated by a space as specified in the table. 81 I-I... PAPERS INTENDED FOR IN- TERNAL USE. THEY CARRY AN IDENTIFYING NUMBER WHICH INDICATES THEIR TYPE AND THE NUMERICAL CODE OF THE ORIGINATING DEPARTMENT

Preparation and Presentation of Digital Maps in Raster Format

USGS Publications Warehouse

Edwards, K.; Batson, R.M.

1980-01-01

A set of algorithms has been developed at USGS Flagstaff for displaying digital map data in raster format. The set includes: FILLIN, which assigns a specified attribute code to units of a map which have been outlined on a digitizer and converted to raster format; FILBND, which removes the outlines; ZIP, which adds patterns to the map units; and COLOR, which provides a simplified process for creating color separation plates for either photographic or lithographic reproduction. - Authors

A GH-Based Ontology to Support Applications for Automating Decision Support

DTIC Science & Technology

2005-03-01

architecture for a decision support sys - tem. For this reason, it obtains data from, and updates, a database. IDA also wanted the prototype’s architecture...Chief In- formation Officer CoABS Control of Agent Based Sys - tems DBMS Database Management System DoD Department of Defense DTD Document Type...Generic Hub, the Moyeu Générique, and the Generische Nabe , specifying each as a separate service description with property names and values of the GH

Nucleotide sequences of Herpes Simplex Virus type 1 (HSV-1) affecting virus entry, cell fusion, and production of glycoprotein gB (VP7)

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeLuca, N.; Bzik, D.J.; Bond, V.C.

1982-10-30

The tsB5 strain of Herpes Simplex Virus type 1 (HSV-1) contains at least two mutations; one mutation specifies the syncytial phenotype and the other confers temperature sensitivity for virus growth. These functions are known to be located between the prototypic map coordinates 0.30 and 0.42. In this study it was demonstrated that tsB5 enters human embryonic lung (HEL) cells more rapidly than KOS, another strain of HSV-1. The EcoRI restriction fragment F from the KOS strain (map coordinates 0.315 to 0.421) was mapped with eight restriction endonucleases, and 16 recombinant plasmids were constructed which contained varying portions of the KOSmore » genome. Recombinant viruses were generated by marker-rescue and marker-transfer cotransfection procedures, using intact DNA from one strain and a recombinant plasmid containing DNA from the other strain. The region of the crossover between the two nonisogenic strains was inferred by the identification of restriction sites in the recombinants that were characteristic of the parental strains. The recombinants were subjected to phenotypic analysis. Syncytium formation, rate of virus entry, and the production of gB were all separable by the crossovers that produced the recombinants. The KOS sequences which rescue the syncytial phenotype of tsB5 were localized to 1.5 kb (map coordinates 0.345 to 0.355), and the temperature-sensitive mutation was localized to 1.2 kb (0.360 to 0.368), giving an average separation between the mutations of 2.5 kb on the 150-kb genome. DNA sequences that specify a functional domain for virus entry were localized to the nucleotide sequences between the two mutations. All three functions could be encoded by the virus gene specifying the gB glycoprotein.« less

Isolation and measurement of the features of arrays of cell aggregates formed by dielectrophoresis using the user-specified Multi Regions Masking (MRM) technique

NASA Astrophysics Data System (ADS)

Yusvana, Rama; Headon, Denis; Markx, Gerard H.

2009-08-01

The use of dielectrophoresis for the construction of artificial skin tissue with skin cells in follicle-like 3D cell aggregates in well-defined patterns is demonstrated. To analyse the patterns produced and to study their development after their formation a Virtual Instrument (VI) system was developed using the LabVIEW IMAQ Vision Development Module. A series of programming functions (algorithms) was used to isolate the features on the image (in our case; the patterned aggregates) and separate them from all other unwanted regions on the image. The image was subsequently converted into a binary version, covering only the desired microarray regions which could then be analysed by computer for automatic object measurements. The analysis utilized the simple and easy-to-use User-Specified Multi-Regions Masking (MRM) technique, which allows one to concentrate the analysis on the desired regions specified in the mask. This simplified the algorithms for the analysis of images of cell arrays having similar geometrical properties. By having a collection of scripts containing masks of different patterns, it was possible to quickly and efficiently develop sets of custom virtual instruments for the offline or online analysis of images of cell arrays in the database.

A Family of ACO Routing Protocols for Mobile Ad Hoc Networks.

PubMed

Rupérez Cañas, Delfín; Sandoval Orozco, Ana Lucila; García Villalba, Luis Javier; Kim, Tai-Hoon

2017-05-22

In this work, an ACO routing protocol for mobile ad hoc networks based on AntHocNet is specified. As its predecessor, this new protocol, called AntOR, is hybrid in the sense that it contains elements from both reactive and proactive routing. Specifically, it combines a reactive route setup process with a proactive route maintenance and improvement process. Key aspects of the AntOR protocol are the disjoint-link and disjoint-node routes, separation between the regular pheromone and the virtual pheromone in the diffusion process and the exploration of routes, taking into consideration the number of hops in the best routes. In this work, a family of ACO routing protocols based on AntOR is also specified. These protocols are based on protocol successive refinements. In this work, we also present a parallelized version of AntOR that we call PAntOR. Using programming multiprocessor architectures based on the shared memory protocol, PAntOR allows running tasks in parallel using threads. This parallelization is applicable in the route setup phase, route local repair process and link failure notification. In addition, a variant of PAntOR that consists of having more than one interface, which we call PAntOR-MI (PAntOR-Multiple Interface), is specified. This approach parallelizes the sending of broadcast messages by interface through threads.

The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed

PubMed Central

2014-01-01

Background Because amino acid activation is rate-limiting for uncatalyzed protein synthesis, it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I and II) of contemporary aminoacyl-tRNA synthetases (aaRS) now translate the code. Observing that codons for the most highly conserved, Class I catalytic peptides, when read in the reverse direction, are very nearly anticodons for Class II defining catalytic peptides, Rodin and Ohno proposed that the two superfamilies descended from opposite strands of the same ancestral gene. This unusual hypothesis languished for a decade, perhaps because it appeared to be unfalsifiable. Results The proposed sense/antisense alignment makes important predictions. Fragments that align in antiparallel orientations, and contain the respective active sites, should catalyze the same two reactions catalyzed by contemporary synthetases. Recent experiments confirmed that prediction. Invariant cores from both classes, called Urzymes after Ur = primitive, authentic, plus enzyme and representing ~20% of the contemporary structures, can be expressed and exhibit high, proportionate rate accelerations for both amino-acid activation and tRNA acylation. A major fraction (60%) of the catalytic rate acceleration by contemporary synthetases resides in segments that align sense/antisense. Bioinformatic evidence for sense/antisense ancestry extends to codons specifying the invariant secondary and tertiary structures outside the active sites of the two synthetase classes. Peptides from a designed, 46-residue gene constrained by Rosetta to encode Class I and II ATP binding sites with fully complementary sequences both accelerate amino acid activation by ATP ~400 fold. Conclusions Biochemical and bioinformatic results substantially enhance the posterior probability that ancestors of the two synthetase classes arose from opposite strands of the same ancestral gene. The remarkable acceleration by short peptides of the rate-limiting step in uncatalyzed protein synthesis, together with the synergy of synthetase Urzymes and their cognate tRNAs, introduce a new paradigm for the origin of protein catalysts, emphasize the potential relevance of an operational RNA code embedded in the tRNA acceptor stems, and challenge the RNA-World hypothesis. Reviewers This article was reviewed by Dr. Paul Schimmel (nominated by Laura Landweber), Dr. Eugene Koonin and Professor David Ardell. PMID:24927791

The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny

PubMed Central

Sevigny, Joseph L.; Kirouac, Lauren E.; Thomas, William Kelley; Ramsdell, Jordan S.; Lawlor, Kayla E.; Sharifi, Osman; Grewal, Simarvir; Baysdorfer, Christopher; Curr, Kenneth; Naimie, Amanda A.; Okamoto, Kazufusa; Murray, James A.; Newcomb, James M.

2015-01-01

The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group. PMID:25996944

Modeling and Comparison of Options for the Disposal of Excess Weapons Plutonium in Russia

DTIC Science & Technology

2002-04-01

fuel LWR cooling time LWR Pu load rate LWR net destruction frac ~ LWR reactors op life mox core frac Excess Separated Pu HTGR Cycle Pu in Waste LWR MOX...reflecting the cycle used in this type of reactor. For the HTGR , the entire core consists of plutonium fuel , therefore a core fraction is not specified...cooling time Time spent fuel unloaded from HTGR reactor must cool before permanently stored 3 years Mox core fraction Fraction of

The integration of manual and automatic image analysis techniques with supporting ground data in a multistage sampling framework for timber resource inventories: Three examples

NASA Technical Reports Server (NTRS)

Gialdini, M.; Titus, S. J.; Nichols, J. D.; Thomas, R.

1975-01-01

An approach to information acquisition is discussed in the context of meeting user-specified needs in a cost-effective, timely manner through the use of remote sensing data, ground data, and multistage sampling techniques. The roles of both LANDSAT imagery and Skylab photography are discussed as first stages of three separate multistage timber inventory systems and results are given for each system. Emphasis is placed on accuracy and meeting user needs.

Using Software Technology to Specify Abstract Interfaces in VLSI Design.

DTIC Science & Technology

1985-01-01

the information required for the specification should be provided "and nothir- g more." He felt that a chief source of specification failure was...this complexity control objective by mix i g two potentially separable kinds of information, i.e. functional/electrical and scheduling semantics...strength Syntactic: immaterial PINS Name AccFn C/D scim G -Scanln C scout PScanOut D routbar PDataOut D p )sh SShift D p2shbar SHold D plshbar S

Advanced obstacle avoidance for a laser based wheelchair using optimised Bayesian neural networks.

PubMed

Trieu, Hoang T; Nguyen, Hung T; Willey, Keith

2008-01-01

In this paper we present an advanced method of obstacle avoidance for a laser based intelligent wheelchair using optimized Bayesian neural networks. Three neural networks are designed for three separate sub-tasks: passing through a door way, corridor and wall following and general obstacle avoidance. The accurate usable accessible space is determined by including the actual wheelchair dimensions in a real-time map used as inputs to each networks. Data acquisitions are performed separately to collect the patterns required for specified sub-tasks. Bayesian frame work is used to determine the optimal neural network structure in each case. Then these networks are trained under the supervision of Bayesian rule. Experiment results showed that compare to the VFH algorithm our neural networks navigated a smoother path following a near optimum trajectory.

[Biomechanical characteristics of the wiping reflex cycle].

PubMed

Berkinblit, M B; Zharkova, I S; Fel'dman, A G; Fukson, O I

1984-01-01

Multijoint goal-directed hindlimb movements in response to chemical stimulation delivered to different skin sites on the medial back surface (wiping reflex-WR) were filmed and analysed in spinal or intact frogs Rana temporaria. Each WR cycle was divisible into five phases (flexion, lifting, aiming, wiping and extension) usually separated from each other by postural interruptions. One or several of the phases might spontaneously be reduced or deleted at all (e. g. the extension phase), although the WR was still effective. Such a reduction was, as a rule, observed in intact frogs while spinal ones usually exhibited the maximum phase sequence. It is suggested that the central spinal generator of the WR is formed of separate functional blocks each of which specifies a certain interjoint coordination and brings the joints to the central-conditioned equilibrium positions.

CONTINUOUS CHELATION-EXTRACTION PROCESS FOR THE SEPARATION AND PURIFICATION OF METALS

DOEpatents

Thomas, J.R.; Hicks, T.E.; Rubin, B.; Crandall, H.W.

1959-12-01

A continuous process is presented for separating metal values and groups of metal values from each other. A complex mixture. e.g., neutron-irradiated uranium, can be resolved into component parts. In the present process the values are dissolved in an acidic solution and adjusted to the proper oxidation state. Thenceforth the solution is contacted with an extractant phase comprising a fluorinated beta -diketone in an organic solvent under centain pH conditions whereupon plutonium and zirconium are extracted. Plutonium is extracted from the foregoing extract with reducing aqueous solutions or under specified acidic conditions and can be recovered from the aqueous solution. Zirconium is then removed with an oxalic acid aqueous phase. The uranium is recovered from the residual original solution using hexone and hexone-diketone extractants leaving residual fission products in the original solution. The uranium is extracted from the hexone solution with dilute nitric acid. Improved separations and purifications are achieved using recycled scrub solutions and the "self-salting" effect of uranyl ions.

Conjunction of color and form without attention: evidence from an orientation-contingent color aftereffect.

PubMed

Houck, M R; Hoffman, J E

1986-05-01

According to feature-integration theory (Treisman & Gelade, 1980), separable features such as color and shape exist in separate maps in preattentive vision and can be integrated only through the use of spatial attention. Many perceptual aftereffects, however, which are also assumed to reflect the features available in preattentive vision, are sensitive to conjunctions of features. One possible resolution of these views holds that adaptation to conjunctions depends on spatial attention. We tested this proposition by presenting observers with gratings varying in color and orientation. The resulting McCollough aftereffects were independent of whether the adaptation stimuli were presented inside or outside of the focus of spatial attention. Therefore, color and shape appear to be conjoined preattentively, when perceptual aftereffects are used as the measure. These same stimuli, however, appeared to be separable in two additional experiments that required observers to search for gratings of a specified color and orientation. These results show that different experimental procedures may be tapping into different stages of preattentive vision.

Germ Cell-less Promotes Centrosome Segregation to Induce Germ Cell Formation.

PubMed

Lerit, Dorothy A; Shebelut, Conrad W; Lawlor, Kristen J; Rusan, Nasser M; Gavis, Elizabeth R; Schedl, Paul; Deshpande, Girish

2017-01-24

The primordial germ cells (PGCs) specified during embryogenesis serve as progenitors to the adult germline stem cells. In Drosophila, the proper specification and formation of PGCs require both centrosomes and germ plasm, which contains the germline determinants. Centrosomes are microtubule (MT)-organizing centers that ensure the faithful segregation of germ plasm into PGCs. To date, mechanisms that modulate centrosome behavior to engineer PGC development have remained elusive. Only one germ plasm component, Germ cell-less (Gcl), is known to play a role in PGC formation. Here, we show that Gcl engineers PGC formation by regulating centrosome dynamics. Loss of gcl leads to aberrant centrosome separation and elaboration of the astral MT network, resulting in inefficient germ plasm segregation and aborted PGC cellularization. Importantly, compromising centrosome separation alone is sufficient to mimic the gcl loss-of-function phenotypes. We conclude Gcl functions as a key regulator of centrosome separation required for proper PGC development. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Performance Modeling of a Pilot in a Free Flight Mode. 1; A Free Flight Self-Separation Cancellations Due to the Requirement for Procedural Intervention

NASA Technical Reports Server (NTRS)

Ntuen, Celestine A.

1999-01-01

Developments are being made that allow pilots to have more flexibility over the control of their aircraft. This new concept is called Free Flight. Free Flight strives to move the current air traffic system into an age where space technology is used to its fullest potential. Self-separation is one part of the Free Flight system. Self-separation provides pilots the opportunity to choose their own route to reach a specified destination provided that they maintain the 'minimum required separation distance between airplanes. In the event that pilots are unable to maintain separation, controllers will need to have the aircraft separation authority passed back to them. This situation is known as a procedural intervention point. This project attempted to examine and diagnose those particular situations in an effort to avoid reaching a procedural intervention point in the near future. Crews that reached procedural intervention points were compared with crews that made similar maneuver types in the same scenario, but did not reach procedural intervention points. Results showed that there were no significant differences between crews in a high-density acute angle flight conditions. However, significant differences in maneuver times, following the detection of an intruder aircraft and following the time the intruder aircraft came into view, were found in a low-density, acute angle scenario.

Asymmetric structure of five and six membered DNA hairpin loops

NASA Technical Reports Server (NTRS)

Baumann, U.; Chang, S.

1995-01-01

The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

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

PubMed

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.

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

PubMed

Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

2012-01-03

Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg(2+) concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon-anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.

PubMed

Hur, Sun; Stroud, Robert M

2007-04-27

Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.

Discovery and biological characterization of geranylated RNA in bacteria.

PubMed

Dumelin, Christoph E; Chen, Yiyun; Leconte, Aaron M; Chen, Y Grace; Liu, David R

2012-11-01

A general MS-based screen for unusually hydrophobic cellular small molecule-RNA conjugates revealed geranylated RNA in Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella enterica var. Typhimurium. The geranyl group is conjugated to the sulfur atom in two 5-methylaminomethyl-2-thiouridine nucleotides. These geranylated nucleotides occur in the first anticodon position of tRNA(Glu)(UUC), tRNA(Lys)(UUU) and tRNA(Gln)(UUG) at a frequency of up to 6.7% (~400 geranylated nucleotides per cell). RNA geranylation can be increased or abolished by mutation or deletion of the selU (ybbB) gene in E. coli, and purified SelU protein in the presence of geranyl pyrophosphate and tRNA can produce geranylated tRNA. The presence or absence of the geranyl group in tRNA(Glu)(UUC), tRNA(Lys)(UUU) and tRNA(Gln)(UUG) affects codon bias and frameshifting during translation. These RNAs represent the first reported examples of oligoisoprenylated cellular nucleic acids.

The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide.

PubMed

Neuhaus, H; Link, G

1987-01-01

The trnK gene endocing the tRNALys(UUU) has been located on mustard (Sinapis alba) chloroplast DNA, 263 bp upstream of the psbA gene on the same strand. The nucleotide sequence of the trnK gene and its flanking regions as well as the putative transcription start and termination sites are shown. The 5' end of the transcript lies 121 bp upstream of the 5' tRNA coding region and is preceded by procaryotic-type "-10" and "-35" sequence elements, while the 3' end maps 2.77 kb downstream to a DNA region with possible stemloop secondary structure. The anticodon loop of the tRNALys is interrupted by a 2,574 bp intron containing a long open reading frame, which codes for 524 amino acids. Based on conserved stem and loop structures, this intron has characteristic features of a class II intron. A region near the carboxyl terminus of the derived polypeptide appears structurally related to maturases.

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

PubMed

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

2018-03-01

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

Changes at work and employee reactions: organizational elements, job insecurity, and short-term stress as predictors for employee health and safety.

PubMed

Størseth, Fred

2006-12-01

The objective was to identify focus areas for possible reduction of job insecurity and its outcomes. A model was specified and tested as a prediction model for health and safety. First, a parsimonious model was specified. The model consisted of perceived job insecurity (as a stressor), organizational factors (information quality, leadership style, work task administration), and short-term stress reactions (job dissatisfaction, reduced work motivation). Second, the model was tested as a prediction model in three separate path analyses, in order to examine the model's contribution in explaining (1) physical health complaints, (2) mental health complaints, and (3) risk taking behavior. A quota sample of Norwegian employees (N= 1,002) was obtained by means of a self-completion questionnaire survey. The results of the structural equation modeling (path analyses) supported the hypothesized model. Mental health complaints and employee risk taking behavior were significantly predicted (not physical health complaints).

LWPC: Long Wavelength Propagation Capability

NASA Astrophysics Data System (ADS)

U. S. Navy; Ferguson, J. A.; Hutchins, Michael

2018-03-01

Long Wavelength Propagation Capability (LWPC), written as a collection of separate programs that perform unique actions, generates geographical maps of signal availability for coverage analysis. The program makes it easy to set up these displays by automating most of the required steps. The user specifies the transmitter location and frequency, the orientation of the transmitting and receiving antennae, and the boundaries of the operating area. The program automatically selects paths along geographic bearing angles to ensure that the operating area is fully covered. The diurnal conditions and other relevant geophysical parameters are then determined along each path. After the mode parameters along each path are determined, the signal strength along each path is computed. The signal strength along the paths is then interpolated onto a grid overlying the operating area. The final grid of signal strength values is used to display the signal-strength in a geographic display. The LWPC uses character strings to control programs and to specify options. The control strings have the same meaning and use among all the programs.

Reliability, precision, and measurement in the context of data from ability tests, surveys, and assessments

NASA Astrophysics Data System (ADS)

Fisher, W. P., Jr.; Elbaum, B.; Coulter, A.

2010-07-01

Reliability coefficients indicate the proportion of total variance attributable to differences among measures separated along a quantitative continuum by a testing, survey, or assessment instrument. Reliability is usually considered to be influenced by both the internal consistency of a data set and the number of items, though textbooks and research papers rarely evaluate the extent to which these factors independently affect the data in question. Probabilistic formulations of the requirements for unidimensional measurement separate consistency from error by modelling individual response processes instead of group-level variation. The utility of this separation is illustrated via analyses of small sets of simulated data, and of subsets of data from a 78-item survey of over 2,500 parents of children with disabilities. Measurement reliability ultimately concerns the structural invariance specified in models requiring sufficient statistics, parameter separation, unidimensionality, and other qualities that historically have made quantification simple, practical, and convenient for end users. The paper concludes with suggestions for a research program aimed at focusing measurement research more on the calibration and wide dissemination of tools applicable to individuals, and less on the statistical study of inter-variable relations in large data sets.

High performance aqueous symmetric supercapacitors based on advanced carbon electrodes and hydrophilic poly(vinylidene fluoride) porous separator

NASA Astrophysics Data System (ADS)

Xie, Qinxing; Huang, Xiaolin; Zhang, Yufeng; Wu, Shihua; Zhao, Peng

2018-06-01

The main components of a supercapacitor include two electrodes, electrolyte, and a separator, which are all essential to specify the energy storage capability of the device. In this work, two kinds of porous carbon materials have been fabricated via different routes using pomelo peel as raw material. The specific surface area are 1187 m2 g-1 for the nanosized worm-like carbon, and 1744 m2 g-1 for the nitrogen-enriched microsized carbon. Both carbon materials demonstrate excellent energy storage capability as electrodes for aqueous supercapacitors. According to the three-electrode measurements, the worm-like carbon exhibits a high specific capacitance of 316 F g-1 at 0.2 A g-1 in 6 M KOH, while the other exhibits 471 F g-1 due to the highly enriched nitrogen atoms in structure. In addition, two-electrode coin-type cells have been assembled with the carbon materials as electrodes and hydrophilic poly(vinylidene fluoride) porous membrane as the separator. The assembled cells exhibit high specific capacitances, excellent rate performance and superior cycling durability because of a synergistic effect of the high performance carbon electrodes and hydrophilic porous separator.

A Family of ACO Routing Protocols for Mobile Ad Hoc Networks

PubMed Central

Rupérez Cañas, Delfín; Sandoval Orozco, Ana Lucila; García Villalba, Luis Javier; Kim, Tai-hoon

2017-01-01

In this work, an ACO routing protocol for mobile ad hoc networks based on AntHocNet is specified. As its predecessor, this new protocol, called AntOR, is hybrid in the sense that it contains elements from both reactive and proactive routing. Specifically, it combines a reactive route setup process with a proactive route maintenance and improvement process. Key aspects of the AntOR protocol are the disjoint-link and disjoint-node routes, separation between the regular pheromone and the virtual pheromone in the diffusion process and the exploration of routes, taking into consideration the number of hops in the best routes. In this work, a family of ACO routing protocols based on AntOR is also specified. These protocols are based on protocol successive refinements. In this work, we also present a parallelized version of AntOR that we call PAntOR. Using programming multiprocessor architectures based on the shared memory protocol, PAntOR allows running tasks in parallel using threads. This parallelization is applicable in the route setup phase, route local repair process and link failure notification. In addition, a variant of PAntOR that consists of having more than one interface, which we call PAntOR-MI (PAntOR-Multiple Interface), is specified. This approach parallelizes the sending of broadcast messages by interface through threads. PMID:28531159

Separation of variables in the special diagonal Hamilton-Jacobi equation: Application to the dynamical problem of a particle constrained on a moving surface

NASA Technical Reports Server (NTRS)

Blanchard, D. L.; Chan, F. K.

1973-01-01

For a time-dependent, n-dimensional, special diagonal Hamilton-Jacobi equation a necessary and sufficient condition for the separation of variables to yield a complete integral of the form was established by specifying the admissible forms in terms of arbitrary functions. A complete integral was then expressed in terms of these arbitrary functions and also the n irreducible constants. As an application of the results obtained for the two-dimensional Hamilton-Jacobi equation, analysis was made for a comparatively wide class of dynamical problems involving a particle moving in Euclidean three-dimensional space under the action of external forces but constrained on a moving surface. All the possible cases in which this equation had a complete integral of the form were obtained and these are tubulated for reference.

An Overview of SAL

NASA Technical Reports Server (NTRS)

Bensalem, Saddek; Ganesh, Vijay; Lakhnech, Yassine; Munoz, Cesar; Owre, Sam; Ruess, Harald; Rushby, John; Rusu, Vlad; Saiedi, Hassen; Shankar, N.

2000-01-01

To become practical for assurance, automated formal methods must be made more scalable, automatic, and cost-effective. Such an increase in scope, scale, automation, and utility can be derived from an emphasis on a systematic separation of concerns during verification. SAL (Symbolic Analysis Laboratory) attempts to address these issues. It is a framework for combining different tools to calculate properties of concurrent systems. The heart of SAL is a language, developed in collaboration with Stanford, Berkeley, and Verimag for specifying concurrent systems in a compositional way. Our instantiation of the SAL framework augments PVS with tools for abstraction, invariant generation, program analysis (such as slicing), theorem proving, and model checking to separate concerns as well as calculate properties (i.e., perform, symbolic analysis) of concurrent systems. We. describe the motivation, the language, the tools, their integration in SAL/PAS, and some preliminary experience of their use.

LSST Operations Simulator

NASA Astrophysics Data System (ADS)

Cook, K. H.; Delgado, F.; Miller, M.; Saha, A.; Allsman, R.; Pinto, P.; Gee, P. A.

2005-12-01

We have developed an operations simulator for LSST and used it to explore design and operations parameter space for this large etendue telescope and its ten year survey mission. The design is modular, with separate science programs coded in separate modules. There is a sophisticated telescope module with all motions parametrized for ease of testing different telescope capabilities, e.g. effect of acceleration capabilities of various motors on science output. Sky brightness is calculated as a function of moon phase and separation. A sophisticated exposure time calculator has been developed for LSST which is being incorporated into the simulator to allow specification of S/N requirements. All important parameters for the telescope, the site and the science programs are easily accessible in configuration files. Seeing and cloud data from the three candidate LSST sites are used for our simulations. The simulator has two broad categories of science proposals: sky coverage and transient events. Sky coverage proposals base their observing priorities on a required number of observations for each field in a particular filter with specified conditions (maximum seeing, sky brightness, etc) and one is used for a weak lensing investigation. Transient proposals are highly configurable. A transient proposal can require sequential, multiple exposures in various filters with a specified sequence of filters, and require a particular cadence for multiple revisits to complete an observation sequence. Each science proposal ranks potential observations based upon the internal logic of that proposal. We present the results of a variety of mixed science program observing simulations, showing how varied programs can be carried out simultaneously, with many observations serving multiple science goals. The simulator has shown that LSST can carry out its multiple missions under a variety of conditions. KHC's work was performed under the auspices of the US DOE, NNSA by the Univ. of California, LLNL under contract No. W-7405-Eng-48.

Towards aspect-oriented functional--structural plant modelling.

PubMed

Cieslak, Mikolaj; Seleznyova, Alla N; Prusinkiewicz, Przemyslaw; Hanan, Jim

2011-10-01

Functional-structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty. The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module. The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes. This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs.

Towards aspect-oriented functional–structural plant modelling

PubMed Central

Cieslak, Mikolaj; Seleznyova, Alla N.; Prusinkiewicz, Przemyslaw; Hanan, Jim

2011-01-01

Background and Aims Functional–structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty. Methods The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module. Key Results The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes. Conclusions This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs. PMID:21724653

Design tradeoff studies and sensitivity analysis, appendices B1 - B4. [hybrid electric vehicles

NASA Technical Reports Server (NTRS)

1979-01-01

Documentation is presented for a program which separately computes fuel and energy consumption for the two modes of operation of a hybrid electric vehicle. The distribution of daily travel is specified as input data as well as the weights which the component driving cycles are given in each of the composite cycles. The possibility of weight reduction through the substitution of various materials is considered as well as the market potential for hybrid vehicles. Data relating to battery compartment weight distribution and vehicle handling analysis is tabulated.

Modeling and Negotiating Service Quality

NASA Astrophysics Data System (ADS)

Benbernou, Salima; Brandic, Ivona; Cappiello, Cinzia; Carro, Manuel; Comuzzi, Marco; Kertész, Attila; Kritikos, Kyriakos; Parkin, Michael; Pernici, Barbara; Plebani, Pierluigi

In this chapter the research problems of specifying and negotiating QoS and its corresponding quality documents are analyzed. For this reason, this chapter is separated into two main sections, Section 6.1 and 6.2, with each dedicated to one of the two problems, i.e., QoS specification and negotiation, respectively. Each section has a similar structure: they first introduce the problem and then, in the remaining subsections, review related work. Finally, the chapter ends with Section 6.3, which identifies research gaps and presents potential research challenges in QoS modelling, specification and negotiation.

Decision analysis in clinical cardiology: When is coronary angiography required in aortic stenosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Georgeson, S.; Meyer, K.B.; Pauker, S.G.

1990-03-15

Decision analysis offers a reproducible, explicit approach to complex clinical decisions. It consists of developing a model, typically a decision tree, that separates choices from chances and that specifies and assigns relative values to outcomes. Sensitivity analysis allows exploration of alternative assumptions. Cost-effectiveness analysis shows the relation between dollars spent and improved health outcomes achieved. In a tutorial format, this approach is applied to the decision whether to perform coronary angiography in a patient who requires aortic valve replacement for critical aortic stenosis.

User's Guide for the Updated EST/BEST Software System

NASA Technical Reports Server (NTRS)

Shah, Ashwin

2003-01-01

This User's Guide describes the structure of the IPACS input file that reflects the modularity of each module. The structured format helps the user locate specific input data and manually enter or edit it. The IPACS input file can have any user-specified filename, but must have a DAT extension. The input file may consist of up to six input data blocks; the data blocks must be separated by delimiters beginning with the $ character. If multiple sections are desired, they must be arranged in the order listed.

TSAFE Interface Control Document v 2.0

NASA Technical Reports Server (NTRS)

Paielli, Russell A.; Bach, Ralph E.

2013-01-01

This document specifies the data interface for TSAFE, the Tactical Separation-Assured Flight Environment. TSAFE is a research prototype of a software application program for alerting air traffic controllers to imminent conflicts in enroute airspace. It is intended for Air Route Traffic Control Centers ("Centers") in the U.S. National Airspace System. It predicts trajectories for approximately 3 minutes into the future, searches for conflicts, and sends data about predicted conflicts to the client, which uses the data to alert an air traffic controller of conflicts. TSAFE itself does not provide a graphical user interface.

Recycling isotachophoresis - A novel approach to preparative protein fractionation

NASA Technical Reports Server (NTRS)

Sloan, Jeffrey E.; Thormann, Wolfgang; Bier, Milan; Twitty, Garland E.; Mosher, Richard A.

1986-01-01

The concept of automated recycling isotachophoresis (RITP) as a purification methodology is discussed, in addition to a description of the apparatus. In the present automated RITP, the computer system follows the achievement of steady state using arrays of universal and specific sensors, monitors the position of the front edge of the zone structure, activates the counterflow if the leading boundary passes a specified position along the separation axis, or changes the applied current, accordingly. The system demonstrates high resolution, in addition to higher processing rates than are possible in zone electrophoresis or isoelectric focusing.

The Influence of Uncompensated Solution Resistance on the Determination and Standard Electrochemical Rate Constants Using Cyclic Voltammetry, and Some Comparisons with AC Voltammetry.

DTIC Science & Technology

1987-09-25

rate constants, k2r using cyclic voltametry . The res tss are expressed in terms of systematic deviations oP sapparent measured" rate constants, k~b(app...concentration was taken to be lum unless otherwise noted. The voltammetric sweep rate was set at 20 V sŕ unless specified otherwise. The general procedure...peaks for the negative- and positive-going potential sweeps have opposite signs, the measured cathodic-anodic peak separation, AEp, will clearly be

Archimedean Spiral Pairs with no Electrical Connections as a Passive Wireless Implantable Sensor

PubMed Central

Drazan, John F; Gunko, Aleksandra; Dion, Matthew; Abdoun, Omar; Cady, Nathaniel C; Connor, Kenneth A; Ledet, Eric H

2015-01-01

We have developed, modeled, fabricated, and tested a passive wireless sensor system that exhibits a linear frequency-displacement relationship. The displacement sensor is comprised of two anti-aligned Archimedean coils separated by an insulating dielectric layer. There are no electrical connections between the two coils and there are no onboard electronics. The two coils are inductively and capacitively coupled due to their close proximity. The sensor system is interrogated wirelessly by monitoring the return loss parameter from a vector network analyzer. The resonant frequency of the sensor is dependent on the displacement between the two coils. Due to changes in the inductive and capacitive coupling between the coils at different distances, the resonant frequency is modulated by coil separation. In a specified range, the frequency shift can be linearized with respect to coil separation. Batch fabrication techniques were used to fabricate copper coils for experimental testing with air as the dielectric. Through testing, we validated the performance of sensors as predicted within acceptable errors. Because of its simplicity, this displacement sensor has potential applications for in vivo sensing. PMID:27430033

Plasma separation process. Betacell (BCELL) code, user's manual

NASA Astrophysics Data System (ADS)

Taherzadeh, M.

1987-11-01

The emergence of clearly defined applications for (small or large) amounts of long-life and reliable power sources has given the design and production of betavoltaic systems a new life. Moreover, because of the availability of the Plasma Separation Program, (PSP) at TRW, it is now possible to separate the most desirable radioisotopes for betacell power generating devices. A computer code, named BCELL, has been developed to model the betavoltaic concept by utilizing the available up-to-date source/cell parameters. In this program, attempts have been made to determine the betacell energy device maximum efficiency, degradation due to the emitting source radiation and source/cell lifetime power reduction processes. Additionally, comparison is made between the Schottky and PN junction devices for betacell battery design purposes. Certain computer code runs have been made to determine the JV distribution function and the upper limit of the betacell generated power for specified energy sources. A Ni beta emitting radioisotope was used for the energy source and certain semiconductors were used for the converter subsystem of the betacell system. Some results for a Promethium source are also given here for comparison.

A Criteria Standard for Conflict Resolution: A Vision for Guaranteeing the Safety of Self-Separation in NextGen

NASA Technical Reports Server (NTRS)

Munoz, Cesar; Butler, Ricky; Narkawicz, Anthony; Maddalon, Jeffrey; Hagen, George

2010-01-01

Distributed approaches for conflict resolution rely on analyzing the behavior of each aircraft to ensure that system-wide safety properties are maintained. This paper presents the criteria method, which increases the quality and efficiency of a safety assurance analysis for distributed air traffic concepts. The criteria standard is shown to provide two key safety properties: safe separation when only one aircraft maneuvers and safe separation when both aircraft maneuver at the same time. This approach is complemented with strong guarantees of correct operation through formal verification. To show that an algorithm is correct, i.e., that it always meets its specified safety property, one must only show that the algorithm satisfies the criteria. Once this is done, then the algorithm inherits the safety properties of the criteria. An important consequence of this approach is that there is no requirement that both aircraft execute the same conflict resolution algorithm. Therefore, the criteria approach allows different avionics manufacturers or even different airlines to use different algorithms, each optimized according to their own proprietary concerns.

Relation of structural and vibratory kinematics of the vocal folds to two acoustic measures of breathy voice based on computational modeling

PubMed Central

Samlan, Robin A.; Story, Brad H.

2011-01-01

Purpose To relate vocal fold structure and kinematics to two acoustic measures: cepstral peak prominence (CPP) and the amplitude of the first harmonic relative to the second (H1-H2). Method A computational, kinematic model of the medial surfaces of the vocal folds was used to specify features of vocal fold structure and vibration in a manner consistent with breathy voice. Four model parameters were altered: degree of vocal fold adduction, surface bulging, vibratory nodal point, and supraglottal constriction. CPP and H1-H2 were measured from simulated glottal area, glottal flow and acoustic waveforms and related to the underlying vocal fold kinematics. Results CPP decreased with increased separation of the vocal processes, whereas the nodal point location had little effect. H1-H2 increased as a function of separation of the vocal processes in the range of 1–1.5 mm and decreased with separation > 1.5 mm. Conclusions CPP is generally a function of vocal process separation. H1*-H2* will increase or decrease with vocal process separation based on vocal fold shape, pivot point for the rotational mode, and supraglottal vocal tract shape, limiting its utility as an indicator of breathy voice. Future work will relate the perception of breathiness to vocal fold kinematics and acoustic measures. PMID:21498582

Ion extraction capabilities of two-grid accelerator systems. [for spacecraft propulsion

NASA Technical Reports Server (NTRS)

Rovang, D. C.; Wilbur, P. J.

1984-01-01

An experimental investigation into the ion extraction capabilities of two-grid accelerator systems common to electrostatic ion thrusters is described. A large body of experimental data which facilitates the selection of the accelerator system geometries and operating parameters necessary to maximize the extracted ion current is presented. Results suggest that the impingement-limited perveance is not dramatically affected by reductions in screen hole diameter to 0.5 mm. Impingement-limited performance is shown to depend most strongly on grid separation distance, accelerator hole diameter ratio, the discharge-to-total accelerating voltage ratio, and the net-to-total accelerating voltage ratio. Results obtained at small grid separation ratios suggest a new grid operating condition where high beam current per hole levels are achieved at a specified net accelerating voltage. It is shown that this operating condition is realized at an optimum ratio of net-to-total accelerating voltage ratio which is typically quite high.

A new family of distribution functions for spherical galaxies

NASA Astrophysics Data System (ADS)

Gerhard, Ortwin E.

1991-06-01

The present study describes a new family of anisotropic distribution functions for stellar systems designed to keep control of the orbit distribution at fixed energy. These are quasi-separable functions of energy and angular momentum, and they are specified in terms of a circularity function h(x) which fixes the distribution of orbits on the potential's energy surfaces outside some anisotropy radius. Detailed results are presented for a particular set of radially anisotropic circularity functions h-alpha(x). In the scale-free logarithmic potential, exact analytic solutions are shown to exist for all scale-free circularity functions. Intrinsic and projected velocity dispersions are calculated and the expected properties are presented in extensive tables and graphs. Several applications of the quasi-separable distribution functions are discussed. They include the effects of anisotropy or a dark halo on line-broadening functions, the radial orbit instability in anisotropic spherical systems, and violent relaxation in spherical collapse.

Analysis of Formation Flying in Eccentric Orbits Using Linearized Equations of Relative Motion

NASA Technical Reports Server (NTRS)

Lane, Christopher; Axelrad, Penina

2004-01-01

Geometrical methods for formation flying design based on the analytical solution to Hill's equations have been previously developed and used to specify desired relative motions in near circular orbits. By generating relationships between the vehicles that are intuitive, these approaches offer valuable insight into the relative motion and allow for the rapid design of satellite configurations to achieve mission specific requirements, such as vehicle separation at perigee or apogee, minimum separation, or a specific geometrical shape. Furthermore, the results obtained using geometrical approaches can be used to better constrain numerical optimization methods; allowing those methods to converge to optimal satellite configurations faster. This paper presents a set of geometrical relationships for formations in eccentric orbits, where Hill.s equations are not valid, and shows how these relationships can be used to investigate formation designs and how they evolve with time.

Jet atomization and cavitation induced by interactions between focused ultrasound and a water surfacea)

NASA Astrophysics Data System (ADS)

Tomita, Y.

2014-09-01

Atomization of a jet produced by the interaction of 1 MHz focused ultrasound with a water surface was investigated using high-speed photography. Viewing various aspects of jet behavior, threshold conditions were obtained necessary for water surface elevation and jet breakup, including drop separation and spray formation. In addition, the position of drop atomization, where a single drop separates from the tip of a jet without spraying, showed good correlation with the jet Weber number. For a set of specified conditions, multiple beaded water masses were formed, moving upwards to produce a vigorous jet. Cavitation phenomena occurred near the center of the primary drop-shaped water mass produced at the leading part of the jet; this was accompanied by fine droplets at the neck between the primary and secondary drop-shaped water masses, due to the collapse of capillary waves.

Nonlinear-regression groundwater flow modeling of a deep regional aquifer system

USGS Publications Warehouse

Cooley, Richard L.; Konikow, Leonard F.; Naff, Richard L.

1986-01-01

A nonlinear regression groundwater flow model, based on a Galerkin finite-element discretization, was used to analyze steady state two-dimensional groundwater flow in the areally extensive Madison aquifer in a 75,000 mi2 area of the Northern Great Plains. Regression parameters estimated include intrinsic permeabilities of the main aquifer and separate lineament zones, discharges from eight major springs surrounding the Black Hills, and specified heads on the model boundaries. Aquifer thickness and temperature variations were included as specified functions. The regression model was applied using sequential F testing so that the fewest number and simplest zonation of intrinsic permeabilities, combined with the simplest overall model, were evaluated initially; additional complexities (such as subdivisions of zones and variations in temperature and thickness) were added in stages to evaluate the subsequent degree of improvement in the model results. It was found that only the eight major springs, a single main aquifer intrinsic permeability, two separate lineament intrinsic permeabilities of much smaller values, and temperature variations are warranted by the observed data (hydraulic heads and prior information on some parameters) for inclusion in a model that attempts to explain significant controls on groundwater flow. Addition of thickness variations did not significantly improve model results; however, thickness variations were included in the final model because they are fairly well defined. Effects on the observed head distribution from other features, such as vertical leakage and regional variations in intrinsic permeability, apparently were overshadowed by measurement errors in the observed heads. Estimates of the parameters correspond well to estimates obtained from other independent sources.

CytometryML binary data standards

NASA Astrophysics Data System (ADS)

Leif, Robert C.

2005-03-01

CytometryML is a proposed new Analytical Cytology (Cytomics) data standard, which is based on a common set of XML schemas for encoding flow cytometry and digital microscopy text based data types (metadata). CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. The separation of the large binary data objects (list mode and image data) from the XML description of the metadata permits the metadata to be directly displayed, analyzed, and reported with standard commercial software packages; the direct use of XML languages; and direct interfacing with clinical information systems. The separation of the binary data into its own files simplifies parsing because all extraneous header data has been eliminated. The storage of images as two-dimensional arrays without any extraneous data, such as in the Adobe Photoshop RAW format, facilitates the development by scientists of their own analysis and visualization software. Adobe Photoshop provided the display infrastructure and the translation facility to interconvert between the image data from commercial formats and RAW format. Similarly, the storage and parsing of list mode binary data type with a group of parameters that are specified at compilation time is straight forward. However when the user is permitted at run-time to select a subset of the parameters and/or specify results of mathematical manipulations, the development of special software was required. The use of CytometryML will permit investigators to be able to create their own interoperable data analysis software and to employ commercially available software to disseminate their data.

On the confounds among retest gains and age-cohort differences in the estimation of within-person change in longitudinal studies: a simulation study.

PubMed

Hoffman, Lesa; Hofer, Scott M; Sliwinski, Martin J

2011-12-01

Although longitudinal designs are the only way in which age changes can be directly observed, a recurrent criticism involves to what extent retest effects may downwardly bias estimates of true age-related cognitive change. Considerable attention has been given to the problem of retest effects within mixed effects models that include separate parameters for longitudinal change over time (usually specified as a function of age) and for the impact of retest (specified as a function of number of exposures). Because time (i.e., intervals between assessment) and number of exposures are highly correlated (and are perfectly correlated in equal interval designs) in most longitudinal studies, the separation of effects of within-person change from effects of retest gains is only possible given certain assumptions (e.g., age convergence). To the extent that cross-sectional and longitudinal effects of age differ, obtained estimates of aging and retest may not be informative. The current simulation study investigated the recovery of within-person change (i.e., aging) and retest effects from repeated cognitive testing as a function of number of waves, age range at baseline, and size and direction of age-cohort differences on the intercept and age slope in age-based models of change. Significant bias and Type I error rates in the estimated effects of retest were observed when these convergence assumptions were not met. These simulation results suggest that retest effects may not be distinguishable from effects of aging-related change and age-cohort differences in typical long-term traditional longitudinal designs.

Documentation of a computer program to simulate transient leakage from confining units using the modular finite-difference, ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Leahy, P.P.; Navoy, A.S.

1994-01-01

Transient leakage into or out of a compressible fine-grained confining unit results from ground- water storage changes within the unit. The computer program described in this report provides a new method of simulating transient leakage using the U.S. Geological Survey modular finite- difference ground-water flow model (MODFLOW). The new program is referred to as the Transient- Leakage Package. The Transient-Leakage Package solves integrodifferential equations that describe flow across the upper and lower boundaries of confining units. For each confining unit, vertical hydraulic conductivity, thickness, and specific storage are specified in input arrays. These properties can vary from cell to cell and the confining unit need not be present at all locations in the grid; however, the confining units must be bounded above and below by model layers in which head is calculated or specified. The package was used in an example problem to simulate drawdown around a pumping well in a system with two aquifers separated by a confining unit. For drawdown values in excess of 1 centimeter, the solution using the new package closely matched an exact analytical solution. The problem also was simulated without the new package by using a separate model layer to represent the confining unit. That simulation was refined by using two model layers to represent the confining unit. The simulation using the Transient-Leakage Package was faster and more accurate than either of the simulations using model layers to represent the confining unit.

Nonlinear-Regression Groundwater Flow Modeling of a Deep Regional Aquifer System

NASA Astrophysics Data System (ADS)

Cooley, Richard L.; Konikow, Leonard F.; Naff, Richard L.

1986-12-01

A nonlinear regression groundwater flow model, based on a Galerkin finite-element discretization, was used to analyze steady state two-dimensional groundwater flow in the areally extensive Madison aquifer in a 75,000 mi2 area of the Northern Great Plains. Regression parameters estimated include intrinsic permeabilities of the main aquifer and separate lineament zones, discharges from eight major springs surrounding the Black Hills, and specified heads on the model boundaries. Aquifer thickness and temperature variations were included as specified functions. The regression model was applied using sequential F testing so that the fewest number and simplest zonation of intrinsic permeabilities, combined with the simplest overall model, were evaluated initially; additional complexities (such as subdivisions of zones and variations in temperature and thickness) were added in stages to evaluate the subsequent degree of improvement in the model results. It was found that only the eight major springs, a single main aquifer intrinsic permeability, two separate lineament intrinsic permeabilities of much smaller values, and temperature variations are warranted by the observed data (hydraulic heads and prior information on some parameters) for inclusion in a model that attempts to explain significant controls on groundwater flow. Addition of thickness variations did not significantly improve model results; however, thickness variations were included in the final model because they are fairly well defined. Effects on the observed head distribution from other features, such as vertical leakage and regional variations in intrinsic permeability, apparently were overshadowed by measurement errors in the observed heads. Estimates of the parameters correspond well to estimates obtained from other independent sources.

Locality, reflection, and wave-particle duality

NASA Astrophysics Data System (ADS)

Mugur-Schächter, Mioara

1987-08-01

Bell's theorem is believed to establish that the quantum mechanical predictions do not generally admit a causal representation compatible with Einsten's principle of separability, thereby proving incompatibility between quantum mechanics and relativity. This interpretation is contested via two convergent approaches which lead to a sharp distinction between quantum nonseparability and violation of Einstein's theory of relativity. In a first approach we explicate from the quantum mechanical formalism a concept of “reflected dependence.” Founded on this concept, we produce a causal representation of the quantum mechanical probability measure involved in Bell's proof, which is clearly separable in Einstein's sense, i.e., it does not involve supraluminal velocities, and nevertheless is “nonlocal” in Bell's sense. So Bell locality and Einstein separability are distinct qualifications, and Bell nonlocality (or Bell nonseparability) and Einstein separability are not incompatible. It is then proved explicitly that with respect to the mentioned representation Bell's derivation does not hold. So Bell's derivation does not establish that any Einstein-separable representation is incompatible with quantum mechanics. This first—negative—conclusion is a syntactic fact. The characteristics of the representation and of the reasoning involved in the mentioned counterexample to the usual interpretation of Bell's theorem suggest that the representation used—notwithstanding its ability to bring forth the specified syntactic fact—is not factually true. Factual truth and syntactic properties also have to be radically distinguished in their turn. So, in a second approach, starting from de Broglie's initial relativistic model of a microsystem, a deeper, factually acceptable representation is constructed. The analyses leading to this second representation show that quantum mechanics does indeed involve basically a certain sort of nonseparability, called here de Broglie-Bohr quantum nonseparability. But the de Broglie-Bohr quantum nonseparability is shown to stem directly from the relativistic character of the considerations which led Louis de Broglie to the fundamental relation p = h/λ, thereby being essentially consistent with relativity. As to Einstein separability, it appears to be a still insufficiently specified concept of which a future, improved specification, will probably be explicitly harmonizable with the de Broglie-Bohr quantum nonseparability. The ensemble of the conclusions obtained here brings forth a new concept of causality, a concept of folded, zigzag, reflexive causality, with respect to which the type of causality conceived of up to now appears as a particular case of outstretched, one-way causality. The reflexive causality is found compatible with the results of Aspect's experiment, and it suggests new experiments. Considered globally, the conclusions obtained in the present work might convert the conceptual situation created by Bell's proof into a process of unification of quantum mechanics and relativity.

Application of Fracture Mechanics to Specify the Proof Load Factor for Clamp Band Systems of Launch Vehicles

NASA Astrophysics Data System (ADS)

Singaravelu, J.; Sundaresan, S.; Nageswara Rao, B.

2013-04-01

This article presents a methodology for evaluation of the proof load factor (PLF) for clamp band system (CBS) made of M250 Maraging steel following fracture mechanics principles.CBS is most widely used as a structural element and as a separation system. Using Taguchi's design of experiments and the response surface method (RSM) the compact tension specimens were tested to establish an empirical relation for the failure load ( P max) in terms of the ultimate strength, width, thickness, and initial crack length. The test results of P max closely matched with the developed RSM empirical relation. Crack growth rates of the maraging steel in different environments were examined. Fracture strength (σf) of center surface cracks and through-crack tension specimens are evaluated utilizing the fracture toughness ( K IC). Stress induced in merman band at flight loading conditions is evaluated to estimate the higher load factor and PLF. Statistical safety factor and reliability assessments were made for the specified flaw sizes useful in the development of fracture control plan for CBS of launch vehicles.

Design and utilisation of protocols to characterise dynamic PET uptake of two tracers using basis pursuit.

PubMed

Bell, Christopher; Puttick, Simon; Rose, Stephen; Smith, Jye; Thomas, Paul; Dowson, Nicholas

2017-06-21

Imaging using more than one biological process using PET could be of great utility, but despite previously proposed approaches to dual-tracer imaging, it is seldom performed. The alternative of performing multiple scans is often infeasible for clinical practice or even in research studies. Dual-tracer PET scanning allows for multiple PET radiotracers to be imaged within the same imaging session. In this paper we describe our approach to utilise the basis pursuit method to aid in the design of dual-tracer PET imaging experiments, and later in separation of the signals. The advantage of this approach is that it does not require a compartment model architecture to be specified or even that both signals are distinguishable in all cases. This means the method for separating dual-tracer signals can be used for many feasible and useful combinations of biology or radiotracer, once an appropriate scanning protocol has been decided upon. Following a demonstration in separating the signals from two consecutively injected radionuclides in a controlled experiment, phantom and list-mode mouse experiments demonstrated the ability to test the feasibility of dual-tracer imaging protocols for multiple injection delays. Increases in variances predicted for kinetic macro-parameters V D and K I in brain and tumoral tissue were obtained when separating the synthetically combined data. These experiments confirmed previous work using other approaches that injections delays of 10-20 min ensured increases in variance were kept minimal for the test tracers used. On this basis, an actual dual-tracer experiment using a 20 min delay was performed using these radio tracers, with the kinetic parameters (V D and K I ) extracted for each tracer in agreement with the literature. This study supports previous work that dual-tracer PET imaging can be accomplished provided certain constraints are adhered to. The utilisation of basis pursuit techniques, with its removed need to specify a model architecture, allows the feasibility of a range of imaging protocols to be investigated via simulation in a straight-forward manner for a wide range of possible scenarios. The hope is that the ease of utilising this approach during feasibility studies and in practice removes any perceived technical barrier to performing dual-tracer imaging.

Design and utilisation of protocols to characterise dynamic PET uptake of two tracers using basis pursuit

NASA Astrophysics Data System (ADS)

Bell, Christopher; Puttick, Simon; Rose, Stephen; Smith, Jye; Thomas, Paul; Dowson, Nicholas

2017-06-01

Imaging using more than one biological process using PET could be of great utility, but despite previously proposed approaches to dual-tracer imaging, it is seldom performed. The alternative of performing multiple scans is often infeasible for clinical practice or even in research studies. Dual-tracer PET scanning allows for multiple PET radiotracers to be imaged within the same imaging session. In this paper we describe our approach to utilise the basis pursuit method to aid in the design of dual-tracer PET imaging experiments, and later in separation of the signals. The advantage of this approach is that it does not require a compartment model architecture to be specified or even that both signals are distinguishable in all cases. This means the method for separating dual-tracer signals can be used for many feasible and useful combinations of biology or radiotracer, once an appropriate scanning protocol has been decided upon. Following a demonstration in separating the signals from two consecutively injected radionuclides in a controlled experiment, phantom and list-mode mouse experiments demonstrated the ability to test the feasibility of dual-tracer imaging protocols for multiple injection delays. Increases in variances predicted for kinetic macro-parameters V D and K I in brain and tumoral tissue were obtained when separating the synthetically combined data. These experiments confirmed previous work using other approaches that injections delays of 10-20 min ensured increases in variance were kept minimal for the test tracers used. On this basis, an actual dual-tracer experiment using a 20 min delay was performed using these radio tracers, with the kinetic parameters (V D and K I) extracted for each tracer in agreement with the literature. This study supports previous work that dual-tracer PET imaging can be accomplished provided certain constraints are adhered to. The utilisation of basis pursuit techniques, with its removed need to specify a model architecture, allows the feasibility of a range of imaging protocols to be investigated via simulation in a straight-forward manner for a wide range of possible scenarios. The hope is that the ease of utilising this approach during feasibility studies and in practice removes any perceived technical barrier to performing dual-tracer imaging.

The Dirac equation and the normalization of its solutions in a closed Friedmann- Robertson-Walker universe

NASA Astrophysics Data System (ADS)

Finster, Felix; Reintjes, Moritz

2009-05-01

We set up the Dirac equation in a Friedmann-Robertson-Walker geometry and separate the spatial and time variables. In the case of a closed universe, the spatial dependence is solved explicitly, giving rise to a discrete set of solutions. We compute the probability integral and analyze a spacetime normalization integral. This analysis allows us to introduce the fermionic projector in a closed Friedmann-Robertson-Walker geometry and to specify its global normalization as well as its local form. First author supported in part by the Deutsche Forschungsgemeinschaft.

Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.

PubMed Central

Eiler, S; Dock-Bregeon, A; Moulinier, L; Thierry, J C; Moras, D

1999-01-01

The 2.4 A crystal structure of the Escherichia coli aspartyl-tRNA synthetase (AspRS)-tRNA(Asp)-aspartyl-adenylate complex shows the two substrates poised for the transfer of the aspartic acid moiety from the adenylate to the 3'-hydroxyl of the terminal adenosine of the tRNA. A general molecular mechanism is proposed for the second step of the aspartylation reaction that accounts for the observed conformational changes, notably in the active site pocket. The stabilization of the transition state is mediated essentially by two amino acids: the class II invariant arginine of motif 2 and the eubacterial-specific Gln231, which in eukaryotes and archaea is replaced by a structurally non-homologous serine. Two archetypal RNA-protein modes of interactions are observed: the anticodon stem-loop, including the wobble base Q, binds to the N-terminal beta-barrel domain through direct protein-RNA interactions, while the binding of the acceptor stem involves both direct and water-mediated hydrogen bonds in an original recognition scheme. PMID:10562565

Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome

PubMed Central

Guo, Zuojun; Gibson, Meghan; Sitha, Sanyasi; Chu, Steven; Mohanty, Udayan

2011-01-01

The fidelity of translation selection begins with the base pairing of codon-anticodon complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces 30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA. We have proposed that large thermal fluctuations play a crucial role in the selection process. To test this conjecture, we have developed a theoretical technique to determine the probability that the ternary complex, as a result of large thermal fluctuations, forms contacts leading to stabilization of the GTPase activated state. We argue that the configurational searches for such processes are in the tail end of the probability distribution and show that the probability for this event is localized around the most likely configuration. Small variations in the repositioning of cognate relative to near-cognate complexes lead to rate enhancement of the cognate complex. The binding energies of over a dozen unique site-bound magnesium structural motifs are investigated and provide insights into the nature of interaction of divalent metal ions with the ribosome. PMID:21368154

Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success.

PubMed

Xiao, Xingqing; Agris, Paul F; Hall, Carol K

2016-05-01

A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search. © 2016 Wiley Periodicals, Inc.

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure

PubMed Central

Létoquart, Juliette; van Tran, Nhan; Caroline, Vonny; Aleksandrov, Alexey; Lazar, Noureddine; van Tilbeurgh, Herman; Liger, Dominique; Graille, Marc

2015-01-01

Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm5U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity. PMID:26438534

Heteroplasmic mutation in the anticodon-stem of mitochondrial tRNA(Val) causing MNGIE-like gastrointestinal dysmotility and cachexia.

PubMed

Horváth, Rita; Bender, Andreas; Abicht, Angela; Holinski-Feder, Elke; Czermin, Birgit; Trips, Tobias; Schneiderat, Peter; Lochmüller, Hanns; Klopstock, Thomas

2009-05-01

While mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is typically associated with mutations in the nuclear gene encoding for thymidine phosphorylase (ECGF1, TYMP), a similar clinical phenotype was described in patients carrying mutations in the nuclear-encoded polymerase gamma (POLG1) as well as a few mitochondrial tRNA genes. Here we report a novel mutation in the mitochondrial tRNA(Val) (MTTV) gene in a girl presenting with clinical symptoms of MNGIE-like gastrointestinal dysmotility and cachexia. Clinical, histological, biochemical and single cell investigations were performed. The heteroplasmic m.1630A>G mutation was detected in the mitochondrial tRNA(Val) (MTTV) gene in the patient's muscle, blood leukocytes and myoblasts, as well as in blood DNA of the unaffected mother. We provide clinical, biochemical, histological, and molecular genetic evidence on the single cell level for the pathogenicity of this mutation. Our finding adds to the genetic heterogeneity of MNGIE-like gastrointestinal symptoms and highlights the importance of a thorough genetic workup in case of suspected mitochondrial disease.

When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism

PubMed Central

Roy, Hervé; Becker, Hubert Dominique; Reinbolt, Joseph; Kern, Daniel

2003-01-01

Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNAAsn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence- and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism. PMID:12874385

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2012-06-05

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

Structural insights into translational fidelity.

PubMed

Ogle, James M; Ramakrishnan, V

2005-01-01

The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.

Factors beyond Enolase 2 and Mitochondrial Lysyl-tRNA Synthetase Precursor Are Required for tRNA Import into Yeast Mitochondria.

PubMed

Baleva, M V; Meyer, M; Entelis, N; Tarassov, I; Kamenski, P; Masquida, B

2017-11-01

In yeast, the import of tRNA Lys with CUU anticodon (tRK1) relies on a complex mechanism where interaction with enolase 2 (Eno2p) dictates a deep conformational change of the tRNA. This event is believed to mask the tRNA from the cytosolic translational machinery to re-direct it towards the mitochondria. Once near the mitochondrial outer membrane, the precursor of the mitochondrial lysyl-tRNA synthetase (preMsk1p) takes over enolase to carry the tRNA within the mitochondrial matrix, where it is supposed to participate in translation following correct refolding. Biochemical data presented in this report focus on the role of enolase. They show that despite the inability of Eno2p alone to form a complex with tRK1, mitochondrial import can be recapitulated in vitro using fractions of yeast extracts sharing either recombinant or endogenous yeast Eno2p as one of the main components. Taken together, our data suggest the existence of a protein complex containing Eno2p that is involved in RNA mitochondrial import.

Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.

PubMed

Finarov, Igal; Moor, Nina; Kessler, Naama; Klipcan, Liron; Safro, Mark G

2010-03-10

The existence of three types of phenylalanyl-tRNA synthetase (PheRS), bacterial (alphabeta)(2), eukaryotic/archaeal cytosolic (alphabeta)(2), and mitochondrial alpha, is a prominent example of structural diversity within the aaRS family. PheRSs have considerably diverged in primary sequences, domain compositions, and subunit organizations. Loss of the anticodon-binding domain B8 in human cytosolic PheRS (hcPheRS) is indicative of variations in the tRNA(Phe) binding and recognition as compared to bacterial PheRSs. We report herein the crystal structure of hcPheRS in complex with phenylalanine at 3.3 A resolution. A novel structural module has been revealed at the N terminus of the alpha subunit. It stretches out into the solvent of approximately 80 A and is made up of three structural domains (DBDs) possessing DNA-binding fold. The dramatic reduction of aminoacylation activity for truncated N terminus variants coupled with structural data and tRNA-docking model testify that DBDs play crucial role in hcPheRS activity.

Pea chloroplast tRNA(Lys) (UUU) gene: transcription and analysis of an intron-containing gene.

PubMed

Boyer, S K; Mullet, J E

1988-07-01

The pea chloroplast trnK gene which encodes tRNA(Lys) (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3'-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5'-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5'-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5' and 3' ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNA(Lys) leads to rapid degradation of intron sequences.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

PubMed Central

Wald, Naama; Alroy, Maya; Botzman, Maya; Margalit, Hanah

2012-01-01

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. PMID:22581775

Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brullé, 1832) (Hymenoptera: Cimbicidae): rearrangements in the IQM and ARNS1EF gene clusters.

PubMed

Doğan, Özgül; Korkmaz, E Mahir

2017-10-01

The Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899 bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T- stop codon. All tRNA genes preferred usual anticodons. Compared with the inferred insect ancestral mitogenome, two tRNA rearrangements were observed in the IQM and ARNS1EF gene clusters, representing a new event not previously reported in Symphyta. An illicit priming of replication and/or intra/inter-mitochondrial recombination and TDRL seem to be responsible mechanisms for the rearrangement events in these gene clusters. Phylogenetic analyses confirmed the position of Corynis within Cimbicidae and recovered a relationship of Tenthredinoidea + (Cephoidea + Orussoidea) in Symphyta.

ANZSoilML: An Australian - New Zealand standard for exchange of soil data

NASA Astrophysics Data System (ADS)

Simons, Bruce; Wilson, Peter; Ritchie, Alistair; Cox, Simon

2013-04-01

The Australian-New Zealand soil information exchange standard (ANZSoilML) is a GML-based standard designed to allow the discovery, query and delivery of soil and landscape data via standard Open Geospatial Consortium (OGC) Web Feature Services. ANZSoilML modifies the Australian soil exchange standard (OzSoilML), which is based on the Australian Soil Information Transfer and Evaluation System (SITES) database design and exchange protocols, to meet the New Zealand National Soils Database requirements. The most significant change was the removal of the lists of CodeList terms in OzSoilML, which were based on the field methods specified in the 'Australian Soil and Land Survey Field Handbook'. These were replaced with empty CodeLists as placeholders to external vocabularies to allow the use of New Zealand vocabularies without violating the data model. Testing of the use of these separately governed Australian and New Zealand vocabularies has commenced. ANZSoilML attempts to accommodate the proposed International Organization for Standardization ISO/DIS 28258 standard for soil quality. For the most part, ANZSoilML is consistent with the ISO model, although major differences arise as a result of: • The need to specify the properties appropriate for each feature type; • The inclusion of soil-related 'Landscape' features; • Allowing the mapping of soil surfaces, bodies, layers and horizons, independent of the soil profile; • Allowing specifying the relationships between the various soil features; • Specifying soil horizons as specialisations of soil layers; • Removing duplication of features provided by the ISO Observation & Measurements standard. The International Union of Soil Sciences (IUSS) Working Group on Soil Information Standards (WG-SIS) aims to develop, promote and maintain a standard to facilitate the exchange of soils data and information. Developing an international exchange standard that is compatible with existing and emerging national and regional standards is a considerable challenge. ANZSoilML is proposed as a profile of the more generalised SoilML model being progressed through the IUSS Working Group.

Relation of structural and vibratory kinematics of the vocal folds to two acoustic measures of breathy voice based on computational modeling.

PubMed

Samlan, Robin A; Story, Brad H

2011-10-01

To relate vocal fold structure and kinematics to 2 acoustic measures: cepstral peak prominence (CPP) and the amplitude of the first harmonic relative to the second (H1-H2). The authors used a computational, kinematic model of the medial surfaces of the vocal folds to specify features of vocal fold structure and vibration in a manner consistent with breathy voice. Four model parameters were altered: degree of vocal fold adduction, surface bulging, vibratory nodal point, and supraglottal constriction. CPP and H1-H2 were measured from simulated glottal area, glottal flow, and acoustic waveforms and were related to the underlying vocal fold kinematics. CPP decreased with increased separation of the vocal processes, whereas the nodal point location had little effect. H1-H2 increased as a function of separation of the vocal processes in the range of 1.0 mm to 1.5 mm and decreased with separation > 1.5 mm. CPP is generally a function of vocal process separation. H1*-H2* (see paragraph 6 of article text for an explanation of the asterisks) will increase or decrease with vocal process separation on the basis of vocal fold shape, pivot point for the rotational mode, and supraglottal vocal tract shape, limiting its utility as an indicator of breathy voice. Future work will relate the perception of breathiness to vocal fold kinematics and acoustic measures.

Plasma Separation Process: Betacell (BCELL) code: User's manual. [Bipolar barrier junction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taherzadeh, M.

1987-11-13

The emergence of clearly defined applications for (small or large) amounts of long-life and reliable power sources has given the design and production of betavoltaic systems a new life. Moreover, because of the availability of the plasma separation program, (PSP) at TRW, it is now possible to separate the most desirable radioisotopes for betacell power generating devices. A computer code, named BCELL, has been developed to model the betavoltaic concept by utilizing the available up-to-date source/cell parameters. In this program, attempts have been made to determine the betacell energy device maximum efficiency, degradation due to the emitting source radiation andmore » source/cell lifetime power reduction processes. Additionally, comparison is made between the Schottky and PN junction devices for betacell battery design purposes. Certain computer code runs have been made to determine the JV distribution function and the upper limit of the betacell generated power for specified energy sources. A Ni beta emitting radioisotope was used for the energy source and certain semiconductors were used for the converter subsystem of the betacell system. Some results for a Promethium source are also given here for comparison. 16 refs.« less

Civilian Health and Medical Program of the Uniformed Services (CHAMPUS); TRICARE Reserve Select; TRICARE Dental Program; Early Eligibility for TRICARE for Certain Reserve Component Members. Final rule.

PubMed

2015-09-15

TRICARE Reserve Select (TRS) is a premium-based TRICARE health plan available for purchase worldwide by qualified members of the Ready Reserve and by qualified survivors of TRS members. TRICARE Dental Program (TDP) is a premium-based TRICARE dental plan available for purchase worldwide by qualified Service members. This final rule revises requirements and procedures for the TRS program to specify the appropriate actuarial basis for calculating premiums in addition to making other minor clarifying administrative changes. For a member who is involuntarily separated from the Selected Reserve under other than adverse conditions this final rule provides a time-limited exception that allows TRS coverage in effect to continue for up to 180 days after the date on which the member is separated from the Selected Reserve and TDP coverage in effect to continue for no less than 180 days after the separation date. It also expands early TRICARE eligibility for certain Reserve Component members from a maximum of 90 days to a maximum of 180 days prior to activation in support of a contingency operation for more than 30 days.

Relation of perceived breathiness to laryngeal kinematics and acoustic measures based on computational modeling

PubMed Central

Samlan, Robin A.; Story, Brad H.; Bunton, Kate

2014-01-01

Purpose To determine 1) how specific vocal fold structural and vibratory features relate to breathy voice quality and 2) the relation of perceived breathiness to four acoustic correlates of breathiness. Method A computational, kinematic model of the vocal fold medial surfaces was used to specify features of vocal fold structure and vibration in a manner consistent with breathy voice. Four model parameters were altered: vocal process separation, surface bulging, vibratory nodal point, and epilaryngeal constriction. Twelve naïve listeners rated breathiness of 364 samples relative to a reference. The degree of breathiness was then compared to 1) the underlying kinematic profile and 2) four acoustic measures: cepstral peak prominence (CPP), harmonics-to-noise ratio, and two measures of spectral slope. Results Vocal process separation alone accounted for 61.4% of the variance in perceptual rating. Adding nodal point ratio and bulging to the equation increased the explained variance to 88.7%. The acoustic measure CPP accounted for 86.7% of the variance in perceived breathiness, and explained variance increased to 92.6% with the addition of one spectral slope measure. Conclusions Breathiness ratings were best explained kinematically by the degree of vocal process separation and acoustically by CPP. PMID:23785184

Should multiple imputation be the method of choice for handling missing data in randomized trials?

PubMed Central

Sullivan, Thomas R; White, Ian R; Salter, Amy B; Ryan, Philip; Lee, Katherine J

2016-01-01

The use of multiple imputation has increased markedly in recent years, and journal reviewers may expect to see multiple imputation used to handle missing data. However in randomized trials, where treatment group is always observed and independent of baseline covariates, other approaches may be preferable. Using data simulation we evaluated multiple imputation, performed both overall and separately by randomized group, across a range of commonly encountered scenarios. We considered both missing outcome and missing baseline data, with missing outcome data induced under missing at random mechanisms. Provided the analysis model was correctly specified, multiple imputation produced unbiased treatment effect estimates, but alternative unbiased approaches were often more efficient. When the analysis model overlooked an interaction effect involving randomized group, multiple imputation produced biased estimates of the average treatment effect when applied to missing outcome data, unless imputation was performed separately by randomized group. Based on these results, we conclude that multiple imputation should not be seen as the only acceptable way to handle missing data in randomized trials. In settings where multiple imputation is adopted, we recommend that imputation is carried out separately by randomized group. PMID:28034175

Should multiple imputation be the method of choice for handling missing data in randomized trials?

PubMed

Sullivan, Thomas R; White, Ian R; Salter, Amy B; Ryan, Philip; Lee, Katherine J

2016-01-01

The use of multiple imputation has increased markedly in recent years, and journal reviewers may expect to see multiple imputation used to handle missing data. However in randomized trials, where treatment group is always observed and independent of baseline covariates, other approaches may be preferable. Using data simulation we evaluated multiple imputation, performed both overall and separately by randomized group, across a range of commonly encountered scenarios. We considered both missing outcome and missing baseline data, with missing outcome data induced under missing at random mechanisms. Provided the analysis model was correctly specified, multiple imputation produced unbiased treatment effect estimates, but alternative unbiased approaches were often more efficient. When the analysis model overlooked an interaction effect involving randomized group, multiple imputation produced biased estimates of the average treatment effect when applied to missing outcome data, unless imputation was performed separately by randomized group. Based on these results, we conclude that multiple imputation should not be seen as the only acceptable way to handle missing data in randomized trials. In settings where multiple imputation is adopted, we recommend that imputation is carried out separately by randomized group.

Delayed childbearing: determining responsibilities for prime gamete quality.

PubMed

Campagne, Daniel M

2013-01-01

Delayed parenting affects fertility in women and in men, and cryopreservation of oocytes and sperm is becoming the latest trend as a solution for those who want or need to postpone procreation, in an attempt to avoid the damage medical conditions or time itself produces in gametes. Although "social freezing" is considered legitimate, its ethical and social aspects are in need of an overdue medical, public and legal debate. Assisted reproduction and cryopreservation, in combination with womb outsourcing, have opened the door to biological ectogenesis and the subsequent question of whether delayed childbearing means we should formally separate procreation from sexual activity. This article briefly summarizes what cryotechniques are capable of presently and in the near future, to separate fact from fiction. It names the implications for and discusses the practically virgin subject of the underlying responsibilities of delayed parenting techniques towards the child-to-be-not only the unborn but also the not-yet-conceived child. Considering the medical, economic, legal and social consequences of these rapidly growing developments in reproduction, several reasons point at the need to formally separate procreation from sexual activity, specifying responsibilities in the first while respecting personal choice in the second.

Human-In-The-Loop Investigation of Interoperability Between Terminal Sequencing and Spacing, Automated Terminal Proximity Alert, and Wake-Separation Recategorization

NASA Technical Reports Server (NTRS)

Callantine, Todd J.; Bienert, Nancy; Borade, Abhay; Gabriel, Conrad; Gujral, Vimmy; Jobe, Kim; Martin, Lynne; Omar, Faisal; Prevot, Thomas; Mercer, Joey

2016-01-01

A human-in-the-loop simulation study addressed terminal-area controller-workstation interface variations for interoperability between three new capabilities being introduced by the FAA. The capabilities are Terminal Sequencing and Spacing (TSAS), Automated Terminal Proximity Alert (ATPA), and wake-separation recategorization, or 'RECAT.' TSAS provides controllers with Controller-Managed Spacing (CMS) tools, including slot markers, speed advisories, and early/late indications, together with runway assignments and sequence numbers. ATPA provides automatic monitor, warning, and alert cones to inform controllers about spacing between aircraft on approach. ATPA cones are sized according to RECAT, an improved method of specifying wake-separation standards. The objective of the study was to identify potential issues and provide recommendations for integrating TSAS with ATPA and RECAT. Participants controlled arrival traffic under seven different display configurations, then tested an 'exploratory' configuration developed with participant input. All the display conditions were workable and acceptable, but controllers strongly preferred having the CMS tools available on Feeder positions, and both CMS tools and ATPA available on Final positions. Controllers found the integrated systems favorable and liked being able to tailor configurations to individual preferences.

Design and implementation of low complexity wake-up receiver for underwater acoustic sensor networks

NASA Astrophysics Data System (ADS)

Yue, Ming

This thesis designs a low-complexity dual Pseudorandom Noise (PN) scheme for identity (ID) detection and coarse frame synchronization. The two PN sequences for a node are identical and are separated by a specified length of gap which serves as the ID of different sensor nodes. The dual PN sequences are short in length but are capable of combating severe underwater acoustic (UWA) multipath fading channels that exhibit time varying impulse responses up to 100 taps. The receiver ID detection is implemented on a microcontroller MSP430F5529 by calculating the correlation between the two segments of the PN sequence with the specified separation gap. When the gap length is matched, the correlator outputs a peak which triggers the wake-up enable. The time index of the correlator peak is used as the coarse synchronization of the data frame. The correlator is implemented by an iterative algorithm that uses only one multiplication and two additions for each sample input regardless of the length of the PN sequence, thus achieving low computational complexity. The real-time processing requirement is also met via direct memory access (DMA) and two circular buffers to accelerate data transfer between the peripherals and the memory. The proposed dual PN detection scheme has been successfully tested by simulated fading channels and real-world measured channels. The results show that, in long multipath channels with more than 60 taps, the proposed scheme achieves high detection rate and low false alarm rate using maximal-length sequences as short as 31 bits to 127 bits, therefore it is suitable as a low-power wake-up receiver. The future research will integrate the wake-up receiver with Digital Signal Processors (DSP) for payload detection.

[Identification of Dendrobium varieties by Fourier transform infrared spectroscopy combined with spectral retrieval].

PubMed

Liu, Fei; Wang, Yuan-zhong; Deng, Xing-yan; Jin, Hang; Yang, Chun-yan

2014-06-01

The infrared spectral of stems of 165 trees of 23 Dendrobium varieties were obtained by means of Fourier transform infrared spectroscopy technique. The spectra show that the spectra of all the samples were similar, and the main components of stem of Dendrobium is cellulose. By the spectral professional software Omnic8.0, three spectral databases were constructed. Lib01 includes of the average spectral of the first four trees of every variety, while Lib02 and Lib03 are constructed from the first-derivative spectra and the second-derivative spectra of average spectra, separately. The correlation search, the square difference retrieval and the square differential difference retrieval of the spectra are performed with the spectral database Lib01 in the specified range of 1 800-500 cm(-1), and the yield correct rate of 92.7%, 74.5% and 92.7%, respectively. The square differential difference retrieval of the first-derivative spectra and the second-derivative spectra is carried out with Lib02 and Lib03 in the same specified range 1 800-500 cm(-1), and shows correct rate of 93.9% for the former and 90.3% for the later. The results show that the first-derivative spectral retrieval of square differential difference algorithm is more suitabe for discerning Dendrobium varieties, and FTIR combining with the spectral retrieval method can identify different varieties of Dendrobium, and the correlation retrieval, the square differential retrieval, the first-derivative spectra and second-derivative spectra retrieval in the specified spectral range are effective and simple way of distinguishing different varieties of Dendrobium.

Major depressive disorder in DSM-5: implications for clinical practice and research of changes from DSM-IV.

PubMed

Uher, Rudolf; Payne, Jennifer L; Pavlova, Barbara; Perlis, Roy H

2014-06-01

The changes in diagnostic criteria for major depressive disorder (MDD) from the fourth to the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM) may appear small but have important consequences for how the diagnosis is used. In DSM-5, MDD is part of the new "Depressive disorders" section, which is separate from "Bipolar disorders", marking a division in what had been known as "Mood disorders". A small wording change has expanded the core mood criterion to include hopelessness, potentially broadening the diagnosis. The replacement of an operationalized bereavement exclusion with a call for clinical judgment in distinguishing normal reactions to significant loss from a disorder in need of clinical attention makes the diagnosis less objective and complicates investigations of the relationship between adversity and depression. A new persistent depressive disorder category is intended to encompass both dysthymia and chronic depression, but its relationship to MDD is ambiguous with conflicting statements on whether the two diagnoses should be concurrent if both sets of criteria are fulfilled. Clarification is also needed on whether MDD can be concurrent with the new broad "other specified bipolar and related disorders". New specifiers of MDD "with anxious distress" and "with mixed features" allow characterization of additional symptoms. The specifier "with perinatal onset" expands on the DSM-IV "postnatal onset" to include onset during pregnancy. We review the changes in MDD definition, provide guidance on their implementation and discuss their implications for clinical practice and research. © 2013 Wiley Periodicals, Inc.

The processing of linear perspective and binocular information for action and perception.

PubMed

Bruggeman, Hugo; Yonas, Albert; Konczak, Jürgen

2007-04-08

To investigate the processing of linear perspective and binocular information for action and for the perceptual judgment of depth, we presented viewers with an actual Ames trapezoidal window. The display, when presented perpendicular to the line of sight, provided perspective information for a rectangular window slanted in depth, while binocular information specified a planar surface in the fronto-parallel plane. We compared pointing towards the display-edges with perceptual judgment of their positions in depth as the display orientation was varied under monocular and binocular view. On monocular trials, pointing and depth judgment were based on the perspective information and failed to respond accurately to changes in display orientation because pictorial information did not vary sufficiently to specify the small differences in orientation. For binocular trials, pointing was based on binocular information and precisely matched the changes in display orientation whereas depth judgment was short of such adjustment and based upon both binocular and perspective-specified slant information. The finding, that on binocular trials pointing was considerably less responsive to the illusion than perceptual judgment, supports an account of two separate processing streams in the human visual system, a ventral pathway involved in object recognition and a dorsal pathway that produces visual information for the control of actions. Previously, similar differences between perception and action were explained by an alternate explanation, that is, viewers selectively attend to different parts of a display in the two tasks. The finding that under monocular view participants responded to perspective information in both the action and the perception task rules out the attention-based argument.

Selecting a Separable Parametric Spatiotemporal Covariance Structure for Longitudinal Imaging Data

PubMed Central

George, Brandon; Aban, Inmaculada

2014-01-01

Longitudinal imaging studies allow great insight into how the structure and function of a subject’s internal anatomy changes over time. Unfortunately, the analysis of longitudinal imaging data is complicated by inherent spatial and temporal correlation: the temporal from the repeated measures, and the spatial from the outcomes of interest being observed at multiple points in a patients body. We propose the use of a linear model with a separable parametric spatiotemporal error structure for the analysis of repeated imaging data. The model makes use of spatial (exponential, spherical, and Matérn) and temporal (compound symmetric, autoregressive-1, Toeplitz, and unstructured) parametric correlation functions. A simulation study, inspired by a longitudinal cardiac imaging study on mitral regurgitation patients, compared different information criteria for selecting a particular separable parametric spatiotemporal correlation structure as well as the effects on Type I and II error rates for inference on fixed effects when the specified model is incorrect. Information criteria were found to be highly accurate at choosing between separable parametric spatiotemporal correlation structures. Misspecification of the covariance structure was found to have the ability to inflate the Type I error or have an overly conservative test size, which corresponded to decreased power. An example with clinical data is given illustrating how the covariance structure procedure can be done in practice, as well as how covariance structure choice can change inferences about fixed effects. PMID:25293361

Robo-AO Discovery and Basic Characterization of Wide Multiple Star Systems in the Pleiades, Praesepe, and NGC 2264 Clusters

NASA Astrophysics Data System (ADS)

Hillenbrand, Lynne A.; Zhang, Celia; Riddle, Reed L.; Baranec, Christoph; Ziegler, Carl; Law, Nicholas M.; Stauffer, John

2018-02-01

We identify and roughly characterize 66 candidate binary star systems in the Pleiades, Praesepe, and NGC 2264 star clusters, based on robotic adaptive optics imaging data obtained using Robo-AO at the Palomar 60″ telescope. Only ∼10% of our imaged pairs were previously known. We detect companions at red optical wavelengths, with physical separations ranging from a few tens to a few thousands of au. A three-sigma contrast curve generated for each final image provides upper limits to the brightness ratios for any undetected putative companions. The observations are sensitive to companions with a maximum contrast of ∼6m at larger separations. At smaller separations, the mean (best) raw contrast at 2″ is 3.ͫ8 (6m), at 1″ is 3.ͫ0 (4.ͫ5), and at 0.″5 is 1.ͫ9 (3m). Point-spread function subtraction can recover nearly the full contrast in the closer separations. For detected candidate binary pairs, we report separations, position angles, and relative magnitudes. Theoretical isochrones appropriate to the Pleiades and Praesepe clusters are then used to determine the corresponding binary mass ratios, which range from 0.2 to 0.9 in q={m}2/{m}1. For our sample of roughly solar-mass (FGK type) stars in NGC 2264 and sub-solar-mass (K and early M-type) primaries in the Pleiades and Praesepe, the overall binary frequency is measured at ∼15.5% ± 2%. However, this value should be considered a lower limit to the true binary fraction within the specified separation and mass ratio ranges in these clusters, given that complex and uncertain corrections for sensitivity and completeness have not been applied.

Distribution of polycyclic aromatic hydrocarbons in lime spray dryer ash

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ping Sun; Panuwat Taerakul; Linda K. Weavers

Four lime spray dryer (LSD) ash samples were collected from a spreader stoker boiler and measured for their concentrations of 16 U.S. EPA specified polycyclic aromatic hydrocarbons (PAHs). Results showed that the total measured PAH concentration correlated with the organic carbon content of the LSD ash. Each LSD ash sample was then separated using a 140 mesh sieve into two fractions: a carbon-enriched fraction ({gt}140 mesh) and a lime-enriched fraction ({lt}140 mesh). Unburned carbon was further separated from the carbon-enriched fraction with a lithiumheteropolytungstate (LST) solution. PAH measurements on these different fractions showed that unburned carbon had the highest PAHmore » concentrations followed by the carbon-enriched fraction, indicating that PAHs were primarily associated with the carbonaceous material in LSD ash. However, detectable levels of PAHs were also found in the lime-enriched fraction, suggesting that the fine spray of slaked lime may sorb PAH compounds from the flue gas in the LSD process. 37 refs., 5 figs., 4 tabs.« less

On solving wave equations on fixed bounded intervals involving Robin boundary conditions with time-dependent coefficients

NASA Astrophysics Data System (ADS)

van Horssen, Wim T.; Wang, Yandong; Cao, Guohua

2018-06-01

In this paper, it is shown how characteristic coordinates, or equivalently how the well-known formula of d'Alembert, can be used to solve initial-boundary value problems for wave equations on fixed, bounded intervals involving Robin type of boundary conditions with time-dependent coefficients. A Robin boundary condition is a condition that specifies a linear combination of the dependent variable and its first order space-derivative on a boundary of the interval. Analytical methods, such as the method of separation of variables (SOV) or the Laplace transform method, are not applicable to those types of problems. The obtained analytical results by applying the proposed method, are in complete agreement with those obtained by using the numerical, finite difference method. For problems with time-independent coefficients in the Robin boundary condition(s), the results of the proposed method also completely agree with those as for instance obtained by the method of separation of variables, or by the finite difference method.

A PREFERENCE-OPPORTUNITY-CHOICE FRAMEWORK WITH APPLICATIONS TO INTERGROUP FRIENDSHIP*

PubMed Central

Zeng, Zhen; Xie, Yu

2009-01-01

A longstanding objective of friendship research is to identify the effects of personal preference and structural opportunity on intergroup friendship choice. Although past studies have used various methods to separate preference from opportunity, researchers have not yet systematically compared the properties and implications of these methods. We put forward a general framework for discrete choice, where choice probability is specified as proportional to the product of preference and opportunity. To implement this framework, we propose a modification to the conditional logit model for estimating preference parameters free from the influence of opportunity structure. We then compare our approach to several alternative methods for separating preference and opportunity used in the friendship choice literature. As an empirical example, we test hypotheses of homophily and status asymmetry in friendship choice using data from the National Longitudinal Study of Adolescent Health. The example also demonstrates the approach of conducting a sensitivity analysis to examine how parameter estimates vary by specification of the opportunity structure. PMID:19569394

On orbital allotments for geostationary satellites

NASA Technical Reports Server (NTRS)

Gonsalvez, David J. A.; Reilly, Charles H.; Mount-Campbell, Clark A.

1986-01-01

The following satellite synthesis problem is addressed: communication satellites are to be allotted positions on the geostationary arc so that interference does not exceed a given acceptable level by enforcing conservative pairwise satellite separation. A desired location is specified for each satellite, and the objective is to minimize the sum of the deviations between the satellites' prescribed and desired locations. Two mixed integer programming models for the satellite synthesis problem are presented. Four solution strategies, branch-and-bound, Benders' decomposition, linear programming with restricted basis entry, and a switching heuristic, are used to find solutions to example synthesis problems. Computational results indicate the switching algorithm yields solutions of good quality in reasonable execution times when compared to the other solution methods. It is demonstrated that the switching algorithm can be applied to synthesis problems with the objective of minimizing the largest deviation between a prescribed location and the corresponding desired location. Furthermore, it is shown that the switching heuristic can use no conservative, location-dependent satellite separations in order to satisfy interference criteria.

SIENA Customer Problem Statement and Requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

L. Sauer; R. Clay; C. Adams

2000-08-01

This document describes the problem domain and functional requirements of the SIENA framework. The software requirements and system architecture of SIENA are specified in separate documents (called SIENA Software Requirement Specification and SIENA Software Architecture, respectively). While currently this version of the document describes the problems and captures the requirements within the Analysis domain (concentrating on finite element models), it is our intention to subsequent y expand this document to describe problems and capture requirements from the Design and Manufacturing domains. In addition, SIENA is designed to be extendible to support and integrate elements from the other domains (see SIENAmore » Software Architecture document).« less

Investigation of the Behavior of Hardening Masonry Exposed to Variable Stresses

PubMed Central

Šlivinskas, Tomas; Jonaitis, Bronius; Marčiukaitis, Jonas Gediminas

2018-01-01

This paper analyzes the behavior of masonry under variable loads during execution (construction stage). It specifies the creep coefficient for calcium silicate brick masonry, presenting the research data of masonry deformation under variable and constant long-term loads. The interaction of separate layers of composite material in masonry is introduced and the formulae for determining long-term deformations are offered. The research results of masonry’s compressive strength and deformation properties under variable and constant long-term loads are presented. These are then compared to calculated ones. According to the presented comparison, the calculated long-term deformations coincide quite well with those determined experimentally. PMID:29710802

The evolution of nervous system patterning: insights from sea urchin development

PubMed Central

Angerer, Lynne M.; Yaguchi, Shunsuke; Angerer, Robert C.; Burke, Robert D.

2011-01-01

Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields – the anterior neuroectoderm and the more posterior ciliary band neuroectoderm – during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution. PMID:21828090

Investigation of the Behavior of Hardening Masonry Exposed to Variable Stresses.

PubMed

Šlivinskas, Tomas; Jonaitis, Bronius; Marčiukaitis, Jonas Gediminas; Zavalis, Robertas

2018-04-28

This paper analyzes the behavior of masonry under variable loads during execution (construction stage). It specifies the creep coefficient for calcium silicate brick masonry, presenting the research data of masonry deformation under variable and constant long-term loads. The interaction of separate layers of composite material in masonry is introduced and the formulae for determining long-term deformations are offered. The research results of masonry’s compressive strength and deformation properties under variable and constant long-term loads are presented. These are then compared to calculated ones. According to the presented comparison, the calculated long-term deformations coincide quite well with those determined experimentally.

The weakly coupled fractional one-dimensional Schrödinger operator with index 1 < α <= 2

NASA Astrophysics Data System (ADS)

Hatzinikitas, Agapitos N.

2010-12-01

Considering the space fractional Weyl operator hat{P}^{α } on the separable Hilbert space H=L^2({R},dx) we determine the asymptotic behavior of both the free Green's function and its variation with respect to energy in one dimension for bound states. Later, we specify the Birman-Schwinger representation for the Schrödinger operator hat{H}_g=K_{α }hat{P}^{α }+ghat{V} and extract the finite-rank portion which is essential for the asymptotic expansion of the ground state. Finally, we determine necessary and sufficient conditions for there to be a bound state for small coupling constant g.

Text-message reminders plus incentives increase adherence to antidiabetic medication in adults with type 2 diabetes.

PubMed

Raiff, Bethany R; Jarvis, Brantley P; Dallery, Jesse

2016-12-01

Some adults with Type 2 diabetes mellitus have difficulty adhering to their oral medication regimens. The current study used a multiple baseline design with 3 adults with Type 2 diabetes. Medication taking was monitored remotely in real time via an electronic pill bottle. During the intervention, monetary incentives were delivered contingent on evidence of adherence to taking medication at specified times. Text-message reminders were also sent if medication was not taken. Adherence increased for all participants. Future studies should separate the relative contributions of text-message and incentive components of the intervention. © 2016 Society for the Experimental Analysis of Behavior.

Chemical Kinetics Database

National Institute of Standards and Technology Data Gateway

SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

A science and technology initiative within the office of civilian radioactive waste management

USGS Publications Warehouse

Budnitz, R.J.; Kiess, T.E.; Peters, M.; Duncan, D.

2003-01-01

In 2002, by following a national decision-making process that had been specified in the 1982 Nuclear Waste Policy Act, Yucca Mountain (YM) was designated as the site for the nation's geologic repository for commercial spent nuclear fuel (SNF). The U.S. Department of Energy's (DOE's) Office of Civilian Radioactive Waste Management (OCRWM) must now obtain regulatory approval to construct and operate a repository there, and to develop transportation and infrastructure needed to support operations. The OCRWM has also recently begun a separate Science and Technology (S&T) initiative, whose purposes, beginnings, current projects, and future plans are described here.

Preliminary design data package, appendices C1 and C2

NASA Technical Reports Server (NTRS)

1980-01-01

The HYBRID2 program which computes the fuel and energy consumption of a hybrid vehicle with a bi-modal control strategy over specified component driving cycles is described. Fuel and energy consumption are computed separately for the two modes of operation. The program also computes yearly average fuel and energy consumption using a composite driving cycle which varies as a function of daily travel. The modelling techniques are described, and subroutines and their functions are given. The composition of modern automobiles is discussed along with the energy required to manufacture an American automobile. The energy required to scrap and recycle automobiles is also discussed.

Monopropellant engine investigation for space shuttle reaction control. Volume 2: Design, fabrication, and demonstration test of a catalytic gas generator for the space shuttle APU

NASA Technical Reports Server (NTRS)

1975-01-01

The capability of a catalytic gas generator to meet the requirement specified for the space shuttle APU is established. A full-scale gas generator, designed to operate at a chamber pressure of 750 psia and a flow rate of 0.36 lbm/sec, was fabricated and subjected to three separate life test series. The nickel foam metal used for catalyst retention was investigated. Inspection of the foam metal following the first life test revealed significant degradation. Consequently an investigation was conducted to determine the mechanism of degradation and to provide an improved foam metal.

Photo interpretation key to Michigan land cover/use

NASA Technical Reports Server (NTRS)

Enslin, W. R.; Hudson, W. D.; Lusch, D. P.

1983-01-01

A set of photo interpretation keys is presented to provide a structured approach to the identification of land cover/use categories as specified in the Michigan Resource Inventory Act. The designated categories are urban and; built up lands; agricultural lands; forest land; nonforested land; water bodies; wetlands; and barren land. The keys were developed for use with medium scale (1:20,000 to 1:24,000) color infrared aerial photography. Although each key is generalized in that it relies only upon the most distinguishing photo characteristics in separating the various land cover/use categories, additional interpretation characteristics, distinguishing features and background material are given.

Trace contaminant control simulation computer program, version 8.1

NASA Technical Reports Server (NTRS)

Perry, J. L.

1994-01-01

The Trace Contaminant Control Simulation computer program is a tool for assessing the performance of various process technologies for removing trace chemical contamination from a spacecraft cabin atmosphere. Included in the simulation are chemical and physical adsorption by activated charcoal, chemical adsorption by lithium hydroxide, absorption by humidity condensate, and low- and high-temperature catalytic oxidation. Means are provided for simulating regenerable as well as nonregenerable systems. The program provides an overall mass balance of chemical contaminants in a spacecraft cabin given specified generation rates. Removal rates are based on device flow rates specified by the user and calculated removal efficiencies based on cabin concentration and removal technology experimental data. Versions 1.0 through 8.0 are documented in NASA TM-108409. TM-108409 also contains a source file listing for version 8.0. Changes to version 8.0 are documented in this technical memorandum and a source file listing for the modified version, version 8.1, is provided. Detailed descriptions for the computer program subprograms are extracted from TM-108409 and modified as necessary to reflect version 8.1. Version 8.1 supersedes version 8.0. Information on a separate user's guide is available from the author.

Trajectory Specification for Automation of Terminal Air Traffic Control

NASA Technical Reports Server (NTRS)

Paielli, Russell A.

2016-01-01

"Trajectory specification" is the explicit bounding and control of aircraft tra- jectories such that the position at each point in time is constrained to a precisely defined volume of space. The bounding space is defined by cross-track, along-track, and vertical tolerances relative to a reference trajectory that specifies position as a function of time. The tolerances are dynamic and will be based on the aircraft nav- igation capabilities and the current traffic situation. A standard language will be developed to represent these specifications and to communicate them by datalink. Assuming conformance, trajectory specification can guarantee safe separation for an arbitrary period of time even in the event of an air traffic control (ATC) sys- tem or datalink failure, hence it can help to achieve the high level of safety and reliability needed for ATC automation. As a more proactive form of ATC, it can also maximize airspace capacity and reduce the reliance on tactical backup systems during normal operation. It applies to both enroute airspace and the terminal area around airports, but this paper focuses on arrival spacing in the terminal area and presents ATC algorithms and software for achieving a specified delay of runway arrival time.

Solving Multiple Isolated, Interleaved, and Blended Tasks through Modular Neuroevolution.

PubMed

Schrum, Jacob; Miikkulainen, Risto

2016-01-01

Many challenging sequential decision-making problems require agents to master multiple tasks. For instance, game agents may need to gather resources, attack opponents, and defend against attacks. Learning algorithms can thus benefit from having separate policies for these tasks, and from knowing when each one is appropriate. How well this approach works depends on how tightly coupled the tasks are. Three cases are identified: Isolated tasks have distinct semantics and do not interact, interleaved tasks have distinct semantics but do interact, and blended tasks have regions where semantics from multiple tasks overlap. Learning across multiple tasks is studied in this article with Modular Multiobjective NEAT, a neuroevolution framework applied to three variants of the challenging Ms. Pac-Man video game. In the standard blended version of the game, a surprising, highly effective machine-discovered task division surpasses human-specified divisions, achieving the best scores to date in this game. In isolated and interleaved versions of the game, human-specified task divisions are also successful, though the best scores are surprisingly still achieved by machine discovery. Modular neuroevolution is thus shown to be capable of finding useful, unexpected task divisions better than those apparent to a human designer.

General well function for pumping from a confined, leaky, or unconfined aquifer

NASA Astrophysics Data System (ADS)

Perina, Tomas; Lee, Tien-Chang

2006-02-01

A general well function for groundwater flow toward an extraction well with non-uniform radial flux along the screen and finite-thickness skin, partially penetrating an unconfined, leaky-boundary flux, or confined aquifer is derived via the Laplace and generalized finite Fourier transforms. The mixed boundary condition at the well face is solved as the discretized Fredholm integral equation. The general well function reduces to a uniform radial flux solution as a special case. In the Laplace domain, the relation between the drawdown in the extraction well and flowrate is linear and the formulations for specified flowrate or specified drawdown pumping are interchangeable. The deviation in drawdown of the uniform from non-uniform radial flux solutions depends on the relative positions of the extraction and observation well screens, aquifer properties, and time of observation. In an unconfined aquifer the maximum deviation occurs during the period of delayed drawdown when the effect of vertical flow is most apparent. The skin and wellbore storage in an observation well are included as model parameters. A separate solution is developed for a fully penetrating well with the radial flux being a continuous function of depth.

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

PubMed Central

2011-01-01

Background Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. Results OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. Conclusions OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. Availability http://www.ontocat.org PMID:21619703

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

PubMed

Adamusiak, Tomasz; Burdett, Tony; Kurbatova, Natalja; Joeri van der Velde, K; Abeygunawardena, Niran; Antonakaki, Despoina; Kapushesky, Misha; Parkinson, Helen; Swertz, Morris A

2011-05-29

Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. http://www.ontocat.org.

Time-Varying Loads of Co-Axial Rotor Blade Crossings

NASA Technical Reports Server (NTRS)

Schatzman, Natasha L.; Komerath, Narayanan; Romander, Ethan A.

2017-01-01

The blade crossing event of a coaxial counter-rotating rotor is a potential source of noise and impulsive blade loads. Blade crossings occur many times during each rotor revolution. In previous research by the authors, this phenomenon was analyzed by simulating two airfoils passing each other at specified speeds and vertical separation distances, using the compressible Navier-Stokes solver OVERFLOW. The simulations explored mutual aerodynamic interactions associated with thickness, circulation, and compressibility effects. Results revealed the complex nature of the aerodynamic impulses generated by upperlower airfoil interactions. In this paper, the coaxial rotor system is simulated using two trains of airfoils, vertically offset, and traveling in opposite directions. The simulation represents multiple blade crossings in a rotor revolution by specifying horizontal distances between each airfoil in the train based on the circumferential distance between blade tips. The shed vorticity from prior crossing events will affect each pair of upperlower airfoils. The aerodynamic loads on the airfoil and flow field characteristics are computed before, at, and after each airfoil crossing. Results from the multiple-airfoil simulation show noticeable changes in the airfoil aerodynamics by introducing additional fluctuation in the aerodynamic time history.

Providing Goal-Based Autonomy for Commanding a Spacecraft

NASA Technical Reports Server (NTRS)

Rabideau, Gregg; Chien, Steve; Liu, Ning

2008-01-01

A computer program for use aboard a scientific-exploration spacecraft autonomously selects among goals specified in high-level requests and generates corresponding sequences of low-level commands, understandable by spacecraft systems. (As used here, 'goals' signifies specific scientific observations.) From a dynamic, onboard set of goals that could oversubscribe spacecraft resources, the program selects a non-oversubscribing subset that maximizes a quality metric. In an early version of the program, the requested goals are assumed to have fixed starting times and durations. Goals can conflict by exceeding a limit on either the number of separate goals or the number of overlapping goals making demands on the same resource. The quality metric used in this version is chosen to ensure that a goal will never be replaced by another having lower priority. At any time, goals can be added or removed, or their priorities can be changed, and the 'best' goal will be selected. Once a goal has been selected, the program implements a robust, flexible approach to generation of low-level commands: Rather than generate rigid sequences with fixed starting times, the program specifies flexible sequences that can be altered to accommodate run time variations.

Joint and separate evaluation of risk reduction: impact on sensitivity to risk reduction magnitude in the context of 4 different risk information formats.

PubMed

Gyrd-Hansen, Dorte; Halvorsen, Peder; Nexøe, Jørgen; Nielsen, Jesper; Støvring, Henrik; Kristiansen, Ivar

2011-01-01

When people make choices, they may have multiple options presented simultaneously or, alternatively, have options presented 1 at a time. It has been shown that if decision makers have little experience with or difficulties in understanding certain attributes, these attributes will have greater impact in joint evaluations than in separate evaluations. The authors investigated the impact of separate versus joint evaluations in a health care context in which laypeople were presented with the possibility of participating in risk-reducing drug therapies. In a randomized study comprising 895 subjects aged 40 to 59 y in Odense, Denmark, subjects were randomized to receive information in terms of absolute risk reduction (ARR), relative risk reduction (RRR), number needed to treat (NNT), or prolongation of life (POL), all with respect to heart attack, and they were asked whether they would be willing to receive a specified treatment. Respondents were randomly allocated to valuing the interventions separately (either great effect or small effect) or jointly (small effect and large effect). Joint evaluation reduced the propensity to accept the intervention that offered the smallest effect. Respondents were more sensitive to scale when faced with a joint evaluation for information formats ARR, RRR, and POL but not for NNT. Evaluability bias appeared to be most pronounced for POL and ARR. Risk information appears to be prone to evaluability bias. This suggests that numeric information on health gains is difficult to evaluate in isolation. Consequently, such information may bear too little weight in separate evaluations of risk-reducing interventions.

How Much Can We Learn from a Single Chromatographic Experiment? A Bayesian Perspective.

PubMed

Wiczling, Paweł; Kaliszan, Roman

2016-01-05

In this work, we proposed and investigated a Bayesian inference procedure to find the desired chromatographic conditions based on known analyte properties (lipophilicity, pKa, and polar surface area) using one preliminary experiment. A previously developed nonlinear mixed effect model was used to specify the prior information about a new analyte with known physicochemical properties. Further, the prior (no preliminary data) and posterior predictive distribution (prior + one experiment) were determined sequentially to search towards the desired separation. The following isocratic high-performance reversed-phase liquid chromatographic conditions were sought: (1) retention time of a single analyte within the range of 4-6 min and (2) baseline separation of two analytes with retention times within the range of 4-10 min. The empirical posterior Bayesian distribution of parameters was estimated using the "slice sampling" Markov Chain Monte Carlo (MCMC) algorithm implemented in Matlab. The simulations with artificial analytes and experimental data of ketoprofen and papaverine were used to test the proposed methodology. The simulation experiment showed that for a single and two randomly selected analytes, there is 97% and 74% probability of obtaining a successful chromatogram using none or one preliminary experiment. The desired separation for ketoprofen and papaverine was established based on a single experiment. It was confirmed that the search for a desired separation rarely requires a large number of chromatographic analyses at least for a simple optimization problem. The proposed Bayesian-based optimization scheme is a powerful method of finding a desired chromatographic separation based on a small number of preliminary experiments.

Mathematical Methods of System Analysis in Construction Materials

NASA Astrophysics Data System (ADS)

Garkina, Irina; Danilov, Alexander

2017-10-01

System attributes of construction materials are defined: complexity of an object, integrity of set of elements, existence of essential, stable relations between elements defining integrative properties of system, existence of structure, etc. On the basis of cognitive modelling (intensive and extensive properties; the operating parameters) materials (as difficult systems) and creation of the cognitive map the hierarchical modular structure of criteria of quality is under construction. It actually is a basis for preparation of the specification on development of material (the required organization and properties). Proceeding from a modern paradigm (model of statement of problems and their decisions) of development of materials, levels and modules are specified in structure of material. It when using the principles of the system analysis allows to considered technological process as the difficult system consisting of elements of the distinguished specification level: from atomic before separate process. Each element of system depending on an effective objective is considered as separate system with more detailed levels of decomposition. Among them, semantic and qualitative analyses of an object (are considered a research objective, decomposition levels, separate elements and communications between them come to light). Further formalization of the available knowledge in the form of mathematical models (structural identification) is carried out; communications between input and output parameters (parametrical identification) are defined. Hierarchical structures of criteria of quality are under construction for each allocated level. On her the relevant hierarchical structures of system (material) are under construction. Regularities of structurization and formation of properties, generally are considered at the levels from micro to a macrostructure. The mathematical model of material is represented as set of the models corresponding to private criteria by which separate modules and their levels (the mathematical description, a decision algorithm) are defined. Adequacy is established (compliance of results of modelling to experimental data; is defined by the level of knowledge of process and validity of the accepted assumptions). The global criterion of quality of material is considered as a set of private criteria (properties). Synthesis of material is carried out on the basis of one-criteria optimization on each of the chosen private criteria. Results of one-criteria optimization are used at multicriteria optimization. The methods of developing materials as single-purpose, multi-purpose, including contradictory, systems are indicated. The scheme of synthesis of composite materials as difficult systems is developed. The specified system approach effectively was used in case of synthesis of composite materials with special properties.

Investigation of Dispersed and Dispersed Annular (rivulet or Thin Film) Flow Phase Separation in Tees.

NASA Astrophysics Data System (ADS)

McCreery, Glenn Ernest

An experimental and analytical investigation of dispersed and dispersed-annular (rivulet or thin film) flow phase separation in tees has been successfully completed. The research was directed at, but is not specific to, determining flow conditions, following a loss of coolant accident, in the large rectangular passageways leading to vacuum buildings in the containment envelope of some CANDU nuclear reactors. The primary objectives of the research were to: (1) obtain experimental data to help formulate and test mechanistic analytical models of phase separation, and (2) develop the analytical models in computer programs which predict phase separation from upstream flow and pressure conditions and downstream and side branch pressure boundary conditions. To meet these objectives an air-water experimental apparatus was constructed, and consists of large air blowers attached to a long rectangular duct leading to a tee in the horizontal plane. A variety of phenomena was investigated including, for comparison with computer predictions, air streamlines and eddy boundary geometry, drop size spectra, macroscopic mass balances, liquid rivulet pathlines, and trajectories of drops of known size and velocity. Four separate computer programs were developed to analyze phase separation. Three of the programs are used sequentially to calculate dispersed mist phase separation in a tee. The fourth is used to calculate rivulet or thin film pathlines. Macroscopic mass balances are calculated from a summation of mass balances for drops with representative sizes (and masses) spaced across the drop size spectrum. The programs are tested against experimental data, and accurately predict gas flow fields, drop trajectories, rivulet pathlines and macroscopic mass balances. In addition to development of the computer programs, analysis was performed to specify the scaling of dispersed mist and rivulet or thin film flow, to investigate pressure losses in tees, and the inter-relationship of loss coefficients, contraction coefficients, and eddy geometry. The important transient effects of liquid storage in eddies were also analyzed.

The complete mitochondrial genome of the gall-forming fly, Fergusonina taylori Nelson and Yeates (Diptera: Fergusoninidae).

PubMed

Nelson, Leigh A; Cameron, Stephen L; Yeates, David K

2011-10-01

The monogeneric family Fergusoninidae consists of gall-forming flies that, together with Fergusobia (Tylenchida: Neotylenchidae) nematodes, form the only known mutualistic association between insects and nematodes. In this study, the entire 16,000 bp mitochondrial genome of Fergusonina taylori Nelson and Yeates was sequenced. The circular genome contains one encoding region including 27 genes and one non-coding A+T-rich region. The arrangement of the protein-coding, ribosomal RNA (rRNA) and transfer RNA (tRNA) genes was the same as that found in the ancestral insect. Nucleotide composition is highly A+T biased. All of the protein initiation codons are ATN, except for nad1 which begins with TTT. All 22 tRNA anticodons of F. taylori match those observed in Drosophila yakuba, and all form the typical cloverleaf structure except for tRNA-Ser((AGN)) which lacks a dihydrouridine (DHU) arm. Secondary structural features of the rRNA genes of Fergusonina are similar to those proposed for other insects, with minor modifications. The mitochondrial genome of Fergusonina presented here may prove valuable for resolving the sister group to the Fergusoninidae, and expands the available mtDNA data sources for acalyptrates overall.

Sulfur Modifications of the Wobble U34 in tRNAs and their Intracellular Localization in Eukaryotic Cells

PubMed Central

Nakai, Yumi; Nakai, Masato; Yano, Takato

2017-01-01

The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNALysUUU, tRNAGluUUC, and tRNAGlnUUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s2U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s2U34 formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s2U34 formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs. PMID:28218716

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure.

PubMed

Létoquart, Juliette; van Tran, Nhan; Caroline, Vonny; Aleksandrov, Alexey; Lazar, Noureddine; van Tilbeurgh, Herman; Liger, Dominique; Graille, Marc

2015-12-15

Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

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

2018-03-06

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

Molecular cloning and long terminal repeat sequences of human endogenous retrovirus genes related to types A and B retrovirus genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, M.

1986-06-01

By using a DNA fragment primarily encoding the reverse transcriptase (pol) region of the Syrian hamster intracisternal A particle (IAP; type A retrovirus) gene as a probe, human endogenous retrovirus genes, tentatively termed HERV-K genes, were cloned from a fetal human liver gene library. Typical HERV-K genes were 9.1 or 9.4 kilobases in length, having long terminal repeats (LTRs) of ca. 970 base pairs. Many structural features commonly observed on the retrovirus LTRs, such as the TATAA box, polyadenylation signal, and terminal inverted repeats, were present on each LTR, and a lysine (K) tRNA having a CUU anticodon was identifiedmore » as a presumed primer tRNA. The HERV-K LTR, however, had little sequence homology to either the IAP LTR or other typical oncovirus LTRs. By filter hybridization, the number of HERV-K genes was estimated to be ca. 50 copies per haploid human genome. The cloned mouse mammary tumor virus (type B) gene was found to hybridize with both the HERV-K and IAP genes to essentially the same extent.« less

A specific scenario for the origin of life and the genetic code based on peptide/oligonucleotide interdependence.

PubMed

Griffith, Robert W

2009-12-01

Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and translation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface.

Structural determinants of an internal ribosome entry site that direct translational reading frame selection

PubMed Central

Ren, Qian; Au, Hilda H.T.; Wang, Qing S.; Lee, Seonghoon; Jan, Eric

2014-01-01

The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein and an overlapping +1 frame ORFx. A U–G base pair adjacent to the anticodon-like pseudoknot of the IRES directs +1 frame translation. Here, we show that the U-G base pair is not absolutely required for +1 frame translation. Extensive mutagenesis demonstrates that 0 and +1 frame translation can be uncoupled. Ribonucleic acid (RNA) structural probing analyses reveal that the mutant IRESs adopt distinct conformations. Toeprinting analysis suggests that the reading frame is selected at a step downstream of ribosome assembly. We propose a model whereby the IRES adopts conformations to occlude the 0 frame aminoacyl-tRNA thereby allowing delivery of the +1 frame aminoacyl-tRNA to the A site to initiate translation of ORFx. This study provides a new paradigm for programmed recoding mechanisms that increase the coding capacity of a viral genome. PMID:25038250

Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes

PubMed Central

Crepin, Thibaut; Shalak, Vyacheslav F.; Yaremchuk, Anna D.; Vlasenko, Dmytro O.; McCarthy, Andrew; Negrutskii, Boris S.; Tukalo, Michail A.; El'skaya, Anna V.

2014-01-01

Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon–anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the ‘GTP’- and ‘GDP’-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis. PMID:25326326

Severe epilepsy as the major symptom of new mutations in the mitochondrial tRNA(Phe) gene.

PubMed

Zsurka, G; Hampel, K G; Nelson, I; Jardel, C; Mirandola, S R; Sassen, R; Kornblum, C; Marcorelles, P; Lavoué, S; Lombès, A; Kunz, W S

2010-02-09

To present 2 families with maternally inherited severe epilepsy as the main symptom of mitochondrial disease due to point mutations at position 616 in the mitochondrial tRNA(Phe) (MT-TF) gene. Histologic stainings were performed on skeletal muscle slices from the 2 index patients. Oxidative phosphorylation activity was measured by oxygraphic and spectrophotometric methods. The patients' complete mitochondrial DNA (mtDNA) and the relevant mtDNA region in maternal relatives were sequenced. Muscle histology showed only decreased overall COX staining, while a combined respiratory chain defect, most severely affecting complex IV, was noted in both patients' skeletal muscle. Sequencing of the mtDNA revealed in both patients a mutation at position 616 in the MT-TF gene (T>C or T>G). These mutations disrupt a base pair in the anticodon stem at a highly conserved position. They were apparently homoplasmic in both patients, and had different heteroplasmy levels in the investigated maternal relatives. Deleterious mutations in the mitochondrial tRNA(Phe) may solely manifest with epilepsy when segregating to homoplasmy. They may be overlooked in the absence of lactate accumulation and typical mosaic mitochondrial defects in muscle.

Sulfur Modifications of the Wobble U34 in tRNAs and their Intracellular Localization in Eukaryotic Cells.

PubMed

Nakai, Yumi; Nakai, Masato; Yano, Takato

2017-02-18

The wobble uridine (U 34 ) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNA Lys UUU , tRNA Glu UUC , and tRNA Gln UUG , harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U 34 , respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U 34 (s²U 34 ) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s²U 34 formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s²U 34 formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs.

Fgf and Hh signalling act on a symmetrical pre-pattern to specify anterior and posterior identity in the zebrafish otic placode and vesicle

PubMed Central

Hammond, Katherine L.; Whitfield, Tanya T.

2011-01-01

Specification of the otic anteroposterior axis is one of the earliest patterning events during inner ear development. In zebrafish, Hedgehog signalling is necessary and sufficient to specify posterior otic identity between the 10 somite (otic placode) and 20 somite (early otic vesicle) stages. We now show that Fgf signalling is both necessary and sufficient for anterior otic specification during a similar period, a function that is completely separable from its earlier role in otic placode induction. In lia–/– (fgf3–/–) mutants, anterior otic character is reduced, but not lost altogether. Blocking all Fgf signalling at 10-20 somites, however, using the pan-Fgf inhibitor SU5402, results in the loss of anterior otic structures and a mirror image duplication of posterior regions. Conversely, overexpression of fgf3 during a similar period, using a heat-shock inducible transgenic line, results in the loss of posterior otic structures and a duplication of anterior domains. These phenotypes are opposite to those observed when Hedgehog signalling is altered. Loss of both Fgf and Hedgehog function between 10 and 20 somites results in symmetrical otic vesicles with neither anterior nor posterior identity, which, nevertheless, retain defined poles at the anterior and posterior ends of the ear. These data suggest that Fgf and Hedgehog act on a symmetrical otic pre-pattern to specify anterior and posterior otic identity, respectively. Each signalling pathway has instructive activity: neither acts simply to repress activity of the other, and, together, they appear to be key players in the specification of anteroposterior asymmetries in the zebrafish ear. PMID:21831919

Los Alamos National Laboratory W76 Pit Tube Lifetime Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeln, Terri G.

2012-04-25

A metallurgical study was requested as part of the Los Alamos National Laboratory (LANL) W76-1 life-extension program (LEP) involving a lifetime analysis of type 304 stainless steel pit tubes subject to repeat bending loads during assembly and disassembly operations at BWXT/Pantex. This initial test phase was completed during the calendar years of 2004-2006 and the report not issued until additional recommended tests could be performed. These tests have not been funded to this date and therefore this report is considered final. Tubes were reportedly fabricated according to Rocky Flats specification P14548 - Seamless Type 304 VIM/VAR Stainless Steel Tubing. Tubemore » diameter was specified as 0.125 inches and wall thickness as 0.028 inches. A heat treat condition is not specified and the hardness range specification can be characteristic of both 1/8 and 1/4 hard conditions. Properties of all tubes tested were within specification. Metallographic analysis could not conclusively determine a specified limit to number of bends allowable. A statistical analysis suggests a range of 5-7 bends with a 99.95% confidence limit. See the 'Statistical Analysis' section of this report. The initial phase of this study involved two separate sets of test specimens. The first group was part of an investigation originating in the ESA-GTS [now Gas Transfer Systems (W-7) Group]. After the bend cycle test parameters were chosen (all three required bends subjected to the same amount of bend cycles) and the tubes bent, the investigation was transferred to Terri Abeln (Metallurgical Science and Engineering) for analysis. Subsequently, another limited quantity of tubes became available for testing and were cycled with the same bending fixture, but with different test parameters determined by T. Abeln.« less

Conifer reproductive development involves B-type MADS-box genes with distinct and different activities in male organ primordia.

PubMed

Sundström, Jens; Engström, Peter

2002-07-01

The Norway spruce MADS-box genes DAL11, DAL12 and DAL13 are phylogenetically related to the angiosperm B-function MADS-box genes: genes that act together with A-function genes in specifying petal identity and with C-function genes in specifying stamen identity to floral organs. In this report we present evidence to suggest that the B-gene function in the specification of identity of the pollen-bearing organs has been conserved between conifers and angiosperms. Expression of DAL11 or DAL12 in transgenic Arabidopsis causes phenotypic changes which partly resemble those caused by ectopic expression of the endogenous B-genes. In similar experiments, flowers of Arabidopsis plants expressing DAL13 showed a different homeotic change in that they formed ectopic anthers in whorls one, two or four. We also demonstrate the capacity of the spruce gene products to form homodimers, and that DAL11 and DAL13 may form heterodimers with each other and with the Arabidopsis B-protein AP3, but not with PI, the second B-gene product in Arabidopsis. In situ hybridization experiments show that the conifer B-like genes are expressed specifically in developing pollen cones, but differ in both temporal and spatial distribution patterns. These results suggest that the B-function in conifers is dual and is separated into a meristem identity and an organ identity function, the latter function possibly being independent of an interaction with the C-function. Thus, even though an ancestral B-function may have acted in combination with C to specify micro- and megasporangia, the B-function has evolved differently in conifers and angiosperms.

50 CFR 217.220 - Specified activity and specified geographical region.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Specified activity and specified geographical region. 217.220 Section 217.220 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Elliott Bay Seawall Project § 217.220 Specified activity and specified geographical region. (a...

Aeroacoustic model of a modulation fan with pitching blades as a sound generator.

PubMed

Du, Lin; Jing, Xiaodong; Sun, Xiaofeng; Song, Weihua

2014-10-01

This paper is to develop an aeroacoustic model for a type of modulation fan termed as rotary subwoofer that is capable of radiating low-frequency sound at high sound pressure levels. The rotary subwoofer is modeled as a baffled monopole whose source strength is specified by the fluctuating mass flow rate produced by the pitching blades that rotate at constant speed. An immersed boundary method is established to simulate the detailed unsteady flow around the blades and also to estimate the source strength for the prediction of the far-field sound pressure level (SPL). The numerical simulation shows that the rotary subwoofer can output oscillating air flow that is in phase with the pitching motion of the blades. It is found that flow separation is more likely to occur on the pitching blades at higher modulation frequency, resulting in the reduction of the radiated SPL. Increasing the maximum blade excursion is one of the most effective means to enhance the sound radiation, but this effect can also be compromised by the flow separation. As the modulation frequency increases, correspondingly increasing the rotational speed or using larger blade solidity is beneficial to suppressing the flow separation and thus improving the acoustic performance of the rotary subwoofer.

Selecting a separable parametric spatiotemporal covariance structure for longitudinal imaging data.

PubMed

George, Brandon; Aban, Inmaculada

2015-01-15

Longitudinal imaging studies allow great insight into how the structure and function of a subject's internal anatomy changes over time. Unfortunately, the analysis of longitudinal imaging data is complicated by inherent spatial and temporal correlation: the temporal from the repeated measures and the spatial from the outcomes of interest being observed at multiple points in a patient's body. We propose the use of a linear model with a separable parametric spatiotemporal error structure for the analysis of repeated imaging data. The model makes use of spatial (exponential, spherical, and Matérn) and temporal (compound symmetric, autoregressive-1, Toeplitz, and unstructured) parametric correlation functions. A simulation study, inspired by a longitudinal cardiac imaging study on mitral regurgitation patients, compared different information criteria for selecting a particular separable parametric spatiotemporal correlation structure as well as the effects on types I and II error rates for inference on fixed effects when the specified model is incorrect. Information criteria were found to be highly accurate at choosing between separable parametric spatiotemporal correlation structures. Misspecification of the covariance structure was found to have the ability to inflate the type I error or have an overly conservative test size, which corresponded to decreased power. An example with clinical data is given illustrating how the covariance structure procedure can be performed in practice, as well as how covariance structure choice can change inferences about fixed effects. Copyright © 2014 John Wiley & Sons, Ltd.

Considerations of solar wind dynamics in mapping of Jupiter's auroral features to magnetospheric sources

NASA Astrophysics Data System (ADS)

Gyalay, S.; Vogt, M.; Withers, P.

2015-12-01

Previous studies have mapped locations from the magnetic equator to the ionosphere in order to understand how auroral features relate to magnetospheric sources. Vogt et al. (2011) in particular mapped equatorial regions to the ionosphere by using a method of flux equivalence—requiring that the magnetic flux in a specified region at the equator is equal to the magnetic flux in the region to which it maps in the ionosphere. This is preferred to methods relying on tracing field lines from global Jovian magnetic field models, which are inaccurate beyond 30 Jupiter radii from the planet. That previous study produced a two-dimensional model—accounting for changes with radial distance and local time—of the normal component of the magnetic field in the equatorial region. However, this two-dimensional fit—which aggregated all equatorial data from Pioneer 10, Pioneer 11, Voyager 1, Voyager 2, Ulysses, and Galileo—did not account for temporal variability resulting from changing solar wind conditions. Building off of that project, this study aims to map the Jovian aurora to the magnetosphere for two separate cases: with a nominal magnetosphere, and with a magnetosphere compressed by high solar wind dynamic pressure. Using the Michigan Solar Wind Model (mSWiM) to predict the solar wind conditions upstream of Jupiter, intervals of high solar wind dynamic pressure were separated from intervals of low solar wind dynamic pressure—thus creating two datasets of magnetometer measurements to be used for two separate 2D fits, and two separate mappings.

50 CFR 216.211 - Specified activity and specified geographical region.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Specified activity and specified... Activities Conducted During Offshore Structure Removal Operations on the Outer Continental Shelf in the U.S. Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

50 CFR 216.211 - Specified activity and specified geographical region.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Specified activity and specified... Activities Conducted During Offshore Structure Removal Operations on the Outer Continental Shelf in the U.S. Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

50 CFR 217.170 - Specified activity and specified geographical region.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Specified activity and specified geographical region. 217.170 Section 217.170 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune...

50 CFR 217.170 - Specified activity and specified geographical region.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Specified activity and specified geographical region. 217.170 Section 217.170 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune...

50 CFR 216.250 - Specified activity and specified geographical region.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Specified activity and specified geographical region. 216.250 Section 216.250 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Weapon Missions in the Gulf of Mexico § 216.250 Specified activity and specified geographical region. (a...

50 CFR 217.170 - Specified activity and specified geographical region.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Specified activity and specified geographical region. 217.170 Section 217.170 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune...

50 CFR 217.170 - Specified activity and specified geographical region.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Specified activity and specified geographical region. 217.170 Section 217.170 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL... Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune...

Supporting shared data structures on distributed memory architectures

NASA Technical Reports Server (NTRS)

Koelbel, Charles; Mehrotra, Piyush; Vanrosendale, John

1990-01-01

Programming nonshared memory systems is more difficult than programming shared memory systems, since there is no support for shared data structures. Current programming languages for distributed memory architectures force the user to decompose all data structures into separate pieces, with each piece owned by one of the processors in the machine, and with all communication explicitly specified by low-level message-passing primitives. A new programming environment is presented for distributed memory architectures, providing a global name space and allowing direct access to remote parts of data values. The analysis and program transformations required to implement this environment are described, and the efficiency of the resulting code on the NCUBE/7 and IPSC/2 hypercubes are described.

Statistical evaluation of the Local Lymph Node Assay.

PubMed

Hothorn, Ludwig A; Vohr, Hans-Werner

2010-04-01

In the Local Lymph Node Assay measured endpoints for each animal, such as cell proliferation, cell counts and/or lymph node weight should be evaluated separately. The primary criterion for a positive response is when the estimated stimulation index is larger than a specified relative threshold that is endpoint- and strain-specific. When the lower confidence limit for ratio-to-control comparisons is larger than a relevance threshold, a biologically relevant increase can be concluded according to the proof of hazard. Alternatively, when the upper confidence limit for ratio-to-control comparisons is smaller than a tolerable margin, harmlessness can be concluded according to a proof of safety. Copyright 2009 Elsevier Inc. All rights reserved.

The Transition from Paper to Digital: Lessons for Medical Specialty Societies

PubMed Central

Miller, Donald W.

2008-01-01

Medical specialty societies often serve their membership by publishing paper forms that may simultaneously include practice guidelines, dataset specifications, and suggested layouts. Many times these forms become de facto standards for the specialty but transform poorly to the logic, structure, preciseness, and flexibility needed in modern electronic medical records. This paper analyzes one such form - a prenatal record published by the American College of Obstetricians and Gynecologists - with the intent to elucidate lessons for other specialty societies who might craft their recommendations to be effectively incorporated within modern electronic medical records. Lessons learned include separating datasets from guidelines/recommendations, specifying, codifying, and qualifying atomic data elements, and leaving graphic design to professionals. PMID:18998856

Statistical properties of a cloud ensemble - A numerical study

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Simpson, Joanne; Soong, Su-Tzai

1987-01-01

The statistical properties of cloud ensembles under a specified large-scale environment, such as mass flux by cloud drafts and vertical velocity as well as the condensation and evaporation associated with these cloud drafts, are examined using a three-dimensional numerical cloud ensemble model described by Soong and Ogura (1980) and Tao and Soong (1986). The cloud drafts are classified as active and inactive, and separate contributions to cloud statistics in areas of different cloud activity are then evaluated. The model results compare well with results obtained from aircraft measurements of a well-organized ITCZ rainband that occurred on August 12, 1974, during the Global Atmospheric Research Program's Atlantic Tropical Experiment.

Hypersonic Shock Interactions About a 25 deg/65 deg Sharp Double Cone

NASA Technical Reports Server (NTRS)

Moss, James N.; LeBeau, Gerald J.; Glass, Christopher E.

2002-01-01

This paper presents the results of a numerical study of shock interactions resulting from Mach 10 air flow about a sharp double cone. Computations are made with the direct simulation Monte Carlo (DSMC) method by using two different codes: the G2 code of Bird and the DAC (DSMC Analysis Code) code of LeBeau. The flow conditions are the pretest nominal free-stream conditions specified for the ONERA R5Ch low-density wind tunnel. The focus is on the sensitivity of the interactions to grid resolution while providing information concerning the flow structure and surface results for the extent of separation, heating, pressure, and skin friction.

Simulation of the Focal Spot of the Accelerator Bremsstrahlung Radiation

NASA Astrophysics Data System (ADS)

Sorokin, V.; Bespalov, V.

2016-06-01

Testing of thick-walled objects by bremsstrahlung radiation (BR) is primarily performed via high-energy quanta. The testing parameters are specified by the focal spot size of the high-energy bremsstrahlung radiation. In determining the focal spot size, the high- energy BR portion cannot be experimentally separated from the low-energy BR to use high- energy quanta only. The patterns of BR focal spot formation have been investigated via statistical modeling of the radiation transfer in the target material. The distributions of BR quanta emitted by the target for different energies and emission angles under normal distribution of the accelerated electrons bombarding the target have been obtained, and the ratio of the distribution parameters has been determined.

Silicon production process evaluations

NASA Technical Reports Server (NTRS)

1982-01-01

Engineering design of the third distillation column in the process was accomplished. The initial design is based on a 94.35% recovery of dichlorosilane in the distillate and a 99.9% recovery of trichlorosilane in the bottoms. The specified separation is achieved at a reflux ratio of 15 with 20 trays (equilibrium stages). Additional specifications and results are reported including equipment size, temperatures and pressure. Specific raw material requirements necessary to produce the silicon in the process are presented. The primary raw materials include metallurgical grade silicon, silicon tetrachloride, hydrogen, copper (catalyst) and lime (waste treatment). Hydrogen chloride is produced as by product in the silicon deposition. Cost analysis of the process was initiated during this reporting period.

A field portable mass spectrometer for monitoring organic vapors.

PubMed

Meier, R W

1978-03-01

A portable mass spectrometer has been designed and built under the sponsorship of the US Army for the purpose of monitoring low concentrations of specified organics in the ambient atmosphere. The goals of the development were discrimination, sensitivity, portability, simplicity of operation, economy and convenience. These objectives were met in a system consisting of a computer operated mass spectrometer with a Llewellyn membrane separator inlet system housed in two 26 x 18 x 9 inch aluminum cases with a total weight less than 150 pounds. This system has shown the capability for field detection of hundreds of specific organic vapors at the parts per billion level in the ambient and workplace environments.

Software for Processing of Digitized Astronegatives from Archives and Databases of Virtual Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu. I.; Andruk, V. N.; Kazantseva, L. V.

The paper discusses and illustrates the steps of basic processing of digitized image of astro negatives. Software for obtaining of a rectangular coordinates and photometric values of objects on photographic plates was created in the environment LINUX / MIDAS / ROMAFOT. The program can automatically process the specified number of files in FITS format with sizes up to 20000 x 20000 pixels. Other programs were made in FORTRAN and PASCAL with the ability to work in an environment of LINUX or WINDOWS. They were used for: identification of stars, separation and exclusion of diffraction satellites and double and triple exposures, elimination of image defects, reduction to the equatorial coordinates and magnitudes of a reference catalogs.

Stagewise cognitive development: an application of catastrophe theory.

PubMed

van der Maas, H L; Molenaar, P C

1992-07-01

In this article an overview is given of traditional methodological approaches to stagewise cognitive developmental research. These approaches are evaluated and integrated on the basis of catastrophe theory. In particular, catastrophe theory specifies a set of common criteria for testing the discontinuity hypothesis proposed by Piaget. Separate criteria correspond to distinct methods used in cognitive developmental research. Such criteria are, for instance, the detection of spurts in development, bimodality of test scores, and increased variability of responses during transitional periods. When a genuine stage transition is present, these criteria are expected to be satisfied. A revised catastrophe model accommodating these criteria is proposed for the stage transition in cognitive development from the preoperational to the concrete operational stage.

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

NASA Technical Reports Server (NTRS)

Zenie, Alexandre; Luguern, Jean-Pierre

1987-01-01

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages.

50 CFR 217.70 - Specified activity and specified geographical region.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Vehicle and Missile Launches at Kodiak Launch Complex, Alaska § 217.70 Specified activity and specified... specified in paragraph (b) of this section by U.S. citizens engaged in space vehicle and missile launch...

50 CFR 217.70 - Specified activity and specified geographical region.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Vehicle and Missile Launches at Kodiak Launch Complex, Alaska § 217.70 Specified activity and specified... specified in paragraph (b) of this section by U.S. citizens engaged in space vehicle and missile launch...

50 CFR 217.70 - Specified activity and specified geographical region.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Vehicle and Missile Launches at Kodiak Launch Complex, Alaska § 217.70 Specified activity and specified... specified in paragraph (b) of this section by U.S. citizens engaged in space vehicle and missile launch...

50 CFR 217.70 - Specified activity and specified geographical region.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Vehicle and Missile Launches at Kodiak Launch Complex, Alaska § 217.70 Specified activity and specified... specified in paragraph (b) of this section by U.S. citizens engaged in space vehicle and missile launch...

Criminal social identity and suicide ideation among Pakistani young prisoners.

PubMed

Shagufta, Sonia; Boduszek, Daniel; Dhingra, Katie; Kola-Palmer, Derrol

2015-01-01

Suicidal behaviour is a common in prisoners, yet little is known about the factors that may protect against thoughts of ending one's life. The purpose of this paper is to specify and test a structural model to examine the relationship between three criminal social identity (CSI) dimensions (in-group affect, in-group ties, and cognitive centrality) and suicide ideation while controlling for period of confinement, age, criminal friends, and offense type (violent vs non-violent). Participants were 415 male juvenile offenders incarcerated in prisons in Khyber Pakhtunkhwa Pakistan. A structural model was specified and tested using Mplus to examine the relationships between the three factors of CSI and suicidal thoughts, while controlling for age, offender type, period of confinement, and substance dependence. The model provided an adequate fit for the data, explaining 22 per cent of variance in suicidal thoughts. In-group affect (the level of personal bonding with other criminals) was found to exert a strong protective effect against suicide ideation. The research contributes important information on suicide ideation in Pakistan, an Islamic country in which suicide is considered a sin and subsequently a criminal offence. Results indicate that Juvenile offenders' sense of shared identity may help to prevent the development of thoughts of death by suicide. Consequently, separating and isolating young prisoners may be ill advised.

On the transonic aerodynamics of a compressor blade row

NASA Technical Reports Server (NTRS)

Erickson, J. C., Jr.; Lordi, J. A.; Rae, W. J.

1971-01-01

Linearized analyses have been carried out for the induced velocity and pressure fields within a compressor blade row operating in an infinite annulus at transonic Mach numbers of the flow relative to the blades. In addition, the relationship between the induced velocity and the shape of the mean blade surface has been determined. A computational scheme has been developed for evaluating the blade mean surface ordinates and surface pressure distributions. The separation of the effects of a specified blade thickness distribution from the effects of a specified distribution of the blade lift has been established. In this way, blade mean surface shapes that are necessary for the blades to be locally nonlifting have been computed and are presented for two examples of blades with biconvex parabolic arc sections of radially tapering thickness. Blade shapes that are required to achieve a zero thickness, uniform chordwise loading, constant work spanwise loading are also presented for two examples. In addition, corresponding surface pressure distributions are given. The flow relative to the blade tips has a high subsonic Mach number in the examples that have been computed. The results suggest that at near-sonic relative tip speeds the effective blade shape is dominated by the thickness distribution, with the lift distribution playing only a minor role.

Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development.

PubMed

Keller, Thomas; Abbott, Jessica; Moritz, Thomas; Doerner, Peter

2006-03-01

Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato (Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.

Cell division requires a direct link between microtubule-bound RacGAP and Anillin in the contractile ring.

PubMed

Gregory, Stephen L; Ebrahimi, Saman; Milverton, Joanne; Jones, Whitney M; Bejsovec, Amy; Saint, Robert

2008-01-08

The mitotic microtubule array plays two primary roles in cell division. It acts as a scaffold for the congression and separation of chromosomes, and it specifies and maintains the contractile-ring position. The current model for initiation of Drosophila and mammalian cytokinesis [1-5] postulates that equatorial localization of a RhoGEF (Pbl/Ect2) by a microtubule-associated motor protein complex creates a band of activated RhoA [6], which subsequently recruits contractile-ring components such as actin, myosin, and Anillin [1-3]. Equatorial microtubules are essential for continued constriction, but how they interact with the contractile apparatus is unknown. Here, we report the first direct molecular link between the microtubule spindle and the actomyosin contractile ring. We find that the spindle-associated component, RacGAP50C, which specifies the site of cleavage [1-5], interacts directly with Anillin, an actin and myosin binding protein found in the contractile ring [7-10]. Both proteins depend on this interaction for their localization. In the absence of Anillin, the spindle-associated RacGAP loses its association with the equatorial cortex, and cytokinesis fails. These results account for the long-observed dependence of cytokinesis on the continual presence of microtubules at the cortex.

SOLDESIGN user's manual copyright

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pillsbury, R.D. Jr.

1991-02-01

SOLDESIGN is a general purpose program for calculating and plotting magnetic fields, Lorentz body forces, resistances and inductances for a system of coaxial uniform current density solenoidal elements. The program was originally written in 1980 and has been evolving ever since. SOLDESIGN can be used with either interactive (terminal) or file input. Output can be to the terminal or to a file. All input is free-field with comma or space separators. SOLDESIGN contains an interactive help feature that allows the user to examine documentation while executing the program. Input to the program consists of a sequence of word commands andmore » numeric data. Initially, the geometry of the elements or coils is defined by specifying either the coordinates of one corner of the coil or the coil centroid, a symmetry parameter to allow certain reflections of the coil (e.g., a split pair), the radial and axial builds, and either the overall current density or the total ampere-turns (NI). A more general quadrilateral element is also available. If inductances or resistances are desired, the number of turns must be specified. Field, force, and inductance calculations also require the number of radial current sheets (or integration points). Work is underway to extend the field, force, and, possibly, inductances to non-coaxial solenoidal elements.« less

Intergovernmental Panel on Climate Change (IPCC)\\, Working Group 1, 1994: Modelling Results Relating Future Atmospheric CO2 Concentrations to Industrial Emissions (DB1009)

DOE Data Explorer

Enting, I. G.; Wigley, M. L.; Heimann, M.

1995-01-01

This database contains the results of various projections of the relation between future CO2 concentrations and future industrial emissions. These projections were contributed by groups from a number of countries as part of the scientific assessment for the report, "Radiative Forcing of Climate Change" (1994), issued by Working Group 1 of the Intergovernmental Panel on Climate Change. There were three types of calculations: (1) forward projections, calculating the atmospheric CO2 concentrations resulting from specified emissions scenarios; (2) inverse calculations, determining the emission rates that would be required to achieve stabilization of CO2 concentrations via specified pathways; (3) impulse response function calculations, required for determining Global Warming Potentials. The projections were extrapolations of global carbon cycle models from pre-industrial times (starting at 1765) to 2100 or 2200 A.D. There were two aspects to the exercise: (1) an assessment of the uncertainty due to uncertainties regarding the current carbon budget, and (2) an assessment of the uncertainties arising from differences between models. To separate these effects, a set of standard conditions was used to explore inter-model differences and then a series of sensitivity studies was used to explore the consequences of current uncertainties in the carbon cycle.

Formation of periodic mesoscale structures arranged in a circular symmetry at the silicon surface exposed to radiation of a single femtosecond laser pulse

NASA Astrophysics Data System (ADS)

Romashevskiy, S. A.; Ashitkov, S. I.; Ovchinnikov, A. V.; Kondratenko, P. S.; Agranat, M. B.

2016-06-01

The periodic mesoscale structures arranged in a circular symmetry were found at the silicon surface exposed to radiation of the single femtosecond laser pulse with a Gaussian intensity profile in the ambient air conditions. These peculiar structures have the appearance of the protrusions of ∼10 nm height and of ∼600 nm width (at a FWHM) separately located inside the ablated region with a period of the incident laser wavelength. It was found that their position at the surface corresponds to the specified laser intensity slightly above the ablation threshold. The number of the formed periodic structures varies with the fluence of the incident laser pulse and in our experiments it was found to have changed from one to eleven. We suppose that formation of these mesoscale structures is caused by heating of a microscale volume to the strongly defined temperature. The theoretical model was proposed to explain the obtained data. It assumes that the interference of incident laser radiation with laser-induced surface electromagnetic waves results in generation of periodic distribution of electron temperature. Thus formation of the periodic structures at the specified laser intensity is attributed to periodically modulated absorption of laser energy at a focal laser spot.

Preliminary design for a standard 10 sup 7 bit Solid State Memory (SSM)

NASA Technical Reports Server (NTRS)

Hayes, P. J.; Howle, W. M., Jr.; Stermer, R. L., Jr.

1978-01-01

A modular concept with three separate modules roughly separating bubble domain technology, control logic technology, and power supply technology was employed. These modules were respectively the standard memory module (SMM), the data control unit (DCU), and power supply module (PSM). The storage medium was provided by bubble domain chips organized into memory cells. These cells and the circuitry for parallel data access to the cells make up the SMM. The DCU provides a flexible serial data interface to the SMM. The PSM provides adequate power to enable one DCU and one SMM to operate simultaneously at the maximum data rate. The SSM was designed to handle asynchronous data rates from dc to 1.024 Mbs with a bit error rate less than 1 error in 10 to the eight power bits. Two versions of the SSM, a serial data memory and a dual parallel data memory were specified using the standard modules. The SSM specification includes requirements for radiation hardness, temperature and mechanical environments, dc magnetic field emission and susceptibility, electromagnetic compatibility, and reliability.

A theory and model of conflict detection in air traffic control: incorporating environmental constraints.

PubMed

Loft, Shayne; Bolland, Scott; Humphreys, Michael S; Neal, Andrew

2009-06-01

A performance theory for conflict detection in air traffic control is presented that specifies how controllers adapt decisions to compensate for environmental constraints. This theory is then used as a framework for a model that can fit controller intervention decisions. The performance theory proposes that controllers apply safety margins to ensure separation between aircraft. These safety margins are formed through experience and reflect the biasing of decisions to favor safety over accuracy, as well as expectations regarding uncertainty in aircraft trajectory. In 2 experiments, controllers indicated whether they would intervene to ensure separation between pairs of aircraft. The model closely predicted the probability of controller intervention across the geometry of problems and as a function of controller experience. When controller safety margins were manipulated via task instructions, the parameters of the model changed in the predicted direction. The strength of the model over existing and alternative models is that it better captures the uncertainty and decision biases involved in the process of conflict detection. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Application of the wavenumber jump condition to the normal and oblique interaction of a plane acoustic wave and a plane shock

NASA Technical Reports Server (NTRS)

Kleinstein, G. G.; Gunzburger, M. D.

1977-01-01

The kinematics of normal and oblique interactions between a plane acoustic wave and a plane shock wave are investigated separately using an approach whereby the shock is considered as a sharp discontinuity surface separating two half-spaces, so that the dispersion relation on either side of the shock and the wavenumber jump condition across a discontinuity surface completely specify the kinematics of the problem in the whole space independently of the acoustic-field dynamics. The normal interaction is analyzed for a stationary shock, and the spectral change of the incident wave is investigated. The normal interaction is then examined for the case of a shock wave traveling into an ambient region where an acoustic disturbance is propagating in the opposite direction. Detailed attention is given to the consequences of the existence of a critical shock speed above which the frequency of the transmitted wave becomes negative. Finally, the oblique interaction with a fixed shock is considered, and the existence and nature of the transmitted wave is investigated, particularly as a function of the angle of incidence.

Integrated Hydrogeological Model of the General Separations Area, Vol. 2, Rev. 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

FLACH, GREGORYK.

1999-04-01

The 15 mi2 General Separations Area (GSA) contains more than 35 RCRA and CERCLA waste units, and is the focus of numerous ongoing and anticipated contaminant migration and remedial alternatives studies. To meet the analysis needs of GSA remediation programs, a groundwater flow model of the area based on the FACT code was developed. The model is consistent with detailed characterization and monitoring data through 1996. Model preprocessing has been automated so that future updates and modifications can be performed quickly and efficiently. Most remedial action scenarios can be explicitly simulated, including vertical recirculation wells, vertical barriers, surface caps, pumpingmore » wells at arbitrary locations, specified drawdown within well casings (instead of flowrate), and wetland impacts of remedial actions. The model has a fine scale vertical mesh and heterogeneous conductivity field, and includes the vadose zone. Therefore, the model is well suited to support subsequent contaminant transport simulations. the model can provide a common framework for analyzing groundwater flow, contaminant migration, and remedial alternatives across Environmental Restoration programs within the GSA.« less

Ion extraction capabilities of two-grid accelerator systems. M.S. Thesis

NASA Technical Reports Server (NTRS)

Rovang, D. C.; Wilbur, P. J.

1984-01-01

An experimental investigation into the ion extraction capabilities of two-grid accelerator systems common to electrostatic ion thrusters is described. This work resulted in a large body of experimental data which facilitates the selection of the accelerator system geometries and operating parameters necessary to maximize the extracted ion current. Results suggest that the impingement-limited perveance is not dramatically affected by reductions in screen hole diameter to 0.5 mm. Impingement-limited performance is shown to depend most strongly on grid separation distance, accelerator hole diameter ratio, the discharge-to-total accelerating voltage ratio, and the net-to-total accelerating voltage ratio. Results obtained at small grid separation ratios suggest a new grid operating condition where high beam current per hole levels are achieved at a specified net accelerating voltage. It is shown that this operating condition is realized at an optimum ratio of net-to-total accelerating voltage ratio which is typically quite high. The apparatus developed for this study is also shown to be well suited measuring the electron backstreaming and electrical breakdown characteristics of two-grid accelerator systems.

A seismic data compression system using subband coding

NASA Technical Reports Server (NTRS)

Kiely, A. B.; Pollara, F.

1995-01-01

This article presents a study of seismic data compression techniques and a compression algorithm based on subband coding. The algorithm includes three stages: a decorrelation stage, a quantization stage that introduces a controlled amount of distortion to allow for high compression ratios, and a lossless entropy coding stage based on a simple but efficient arithmetic coding method. Subband coding methods are particularly suited to the decorrelation of nonstationary processes such as seismic events. Adaptivity to the nonstationary behavior of the waveform is achieved by dividing the data into separate blocks that are encoded separately with an adaptive arithmetic encoder. This is done with high efficiency due to the low overhead introduced by the arithmetic encoder in specifying its parameters. The technique could be used as a progressive transmission system, where successive refinements of the data can be requested by the user. This allows seismologists to first examine a coarse version of waveforms with minimal usage of the channel and then decide where refinements are required. Rate-distortion performance results are presented and comparisons are made with two block transform methods.

Standing wave design and experimental validation of a tandem simulated moving bed process for insulin purification.

PubMed

Xie, Yi; Mun, Sungyong; Kim, Jinhyun; Wang, Nien-Hwa Linda

2002-01-01

A tandem simulated moving bed (SMB) process for insulin purification has been proposed and validated experimentally. The mixture to be separated consists of insulin, high molecular weight proteins, and zinc chloride. A systematic approach based on the standing wave design, rate model simulations, and experiments was used to develop this multicomponent separation process. The standing wave design was applied to specify the SMB operating conditions of a lab-scale unit with 10 columns. The design was validated with rate model simulations prior to experiments. The experimental results show 99.9% purity and 99% yield, which closely agree with the model predictions and the standing wave design targets. The agreement proves that the standing wave design can ensure high purity and high yield for the tandem SMB process. Compared to a conventional batch SEC process, the tandem SMB has 10% higher yield, 400% higher throughput, and 72% lower eluant consumption. In contrast, a design that ignores the effects of mass transfer and nonideal flow cannot meet the purity requirement and gives less than 96% yield.

Gene polymorphisms of tumor necrosis factor alpha-308 and interleukin-10-1082 among asthmatic Egyptian children.

PubMed

Zedan, Magdy; Settin, Ahmed; Farag, Mohammad K; El-Bayoumi, Mohammed; El Regal, Mohammed Ezz; El Baz, Rizk; Osman, Engy

2008-01-01

Tumor necrosis factor (TNF) alpha-308 and interleukin (IL)-10(-1082) have potent inflammatory responses in the process of airway inflammation in asthma. The purpose of this study was to check for association of polymorphisms related to cytokine genes with susceptibility and severity of bronchial asthma in Egyptian children. Blood samples of 69 asthmatic children receiving treatment and follow-up at the Allergy and Respiratory Medicine Unit, Mansoura University Children Hospital, Mansoura, Egypt, were subjected to DNA extraction and amplification using polymerase chain reaction with sequence-specific primers for detection of single nucleotide polymorphisms in the promoter regions of cytokine genes TNF-alpha(-308(G-->A)), IL-10(-1082(G-->A)). Compared with normal controls, Egyptian asthmatic children showed a significant higher frequency of IL-10(-1082) G/G homozygosity genotype (p < 0.001; odds ratio [OR] = 7) with lower frequency of G/A heterozygosity genotype among cases. This finding also was detected in cases with persistent asthma and eczema. These cases showed significant lower frequency of TNF-alpha-308 G/A heterozygosity (p < 0.05; OR = 0.44). Also, male cases, cases with positive family history, and those patients with persistent types of asthma showed a higher frequency of TNF-alpha-308 G/G homozygosity. IL-10(-1082(G-->A)) G/G and TNF-alpha-308(G-->A) G/G may be a contributing factor in susceptibility as well as severity of asthma among Egyptian children. Separate studies should be specified relating these cytokine genotypes to response to various modalities in asthma therapy. This study reports that IL-10(-1082(G-->A)) G/G and TNF-alpha-308(G-->A) G/G genotypes may be contributing factors in susceptibility as well as in severity of asthma among Egyptian children. Separate studies may be specified relating these cytokine genotypes to response to various modalities in asthma therapy.

Renewal of an old European Pharmacopoeia method for Terazosin using modeling with mass spectrometric peak tracking.

PubMed

Kormány, Róbert; Molnár, Imre; Fekete, Jenő

2017-02-20

An older method for terazosin was reworked in order to reduce the analysis time from 90min (2×45min) to below 5min. The method in European Pharmacopoeia (Ph.Eur.) investigates the specified impurities separately. The reason of the different methods is that the retention of two impurities is not adequate in reversed phase, not even with 100% water. Therefore ion-pair-chromatography has to be applied and since that two impurities absorb at low UV-wavelength they had to be analyzed by different method than the other specified impurities. In our new method we could improve the retention with pH elevation using a new type of stationary phases available for high pH applications. Also a detection wavelength could be selected that is appropriate for the detection and quantification of all impurities. The method development is the bottleneck of liquid chromatography even today, when more and more fast chromatographic systems are used. Expert knowledge with intelligent programs is available to reduce the time of method development and offer extra information about the robustness of the separation. Design of Experiments (DoE) for simultaneous optimization of gradient time (t G ), temperature (T) and ternary eluent composition (t C ) requires 12 experiments. A good alternative way to identify a certain peak in different chromatograms is the molecular mass of the compound, due to its high specificity. Liquid Chromatography-Mass Spectrometry (LC-MS) is now a routine technique and increasingly available in laboratories. In our experiment for the resolution- and retention modeling the DryLab4 method development software (Version 4.2) was used. In recent versions of the software the use of (m/z)-MS-data is possible along the UV-peak-area-tracking technology. The modelled and measured chromatograms showed excellent correlations. The average retention time deviations were ca. 0.5s and there was no difference between the predicted and measured R s,crit -values. Copyright © 2016. Published by Elsevier B.V.

Determination of D-saccharic acid-1,4-lactone from brewed kombucha broth by high-performance capillary electrophoresis.

PubMed

Wang, Kan; Gan, Xuhua; Tang, Xinyun; Wang, Shuo; Tan, Huarong

2010-02-01

Kombucha is a health tonic. D-saccharic acid-1,4-lactone (DSL), a component of kombucha, inhibits the activity of glucuronidase, an enzyme indirectly related with cancers. To date, there is no efficient method to determine the content of DSL in kombucha samples. In this paper, we report a rapid and simple method for the separation and determination of DSL in kombucha samples, using the high-performance capillary electrophoresis (HPCE) method with diode array detection (DAD). With optimized conditions, DSL can be separated in a 50 cm length capillary at a separation voltage of 20 kV in 40 mmol/L borax buffer (pH 6.5) containing 30 mmol/L SDS and 15% methanol (v/v). Quantitative evaluation of DSL was determined by ultraviolet absorption at lambda=190 nm. The relationship between the peak areas and the DSL concentrations, in a specified working range with linear response, was determined by first-order polynomial regression over the range 50-1500 microg/mL with a detection limit of 17.5 microg/mL. Our method demonstrated excellent reproducibility and accuracy with relative standard deviations (RSD) of less than 5% DSL content (n=5). This is the first report to determine DSL by HPCE. We have successfully applied this method to determine DSL in kombucha samples in various fermented conditions. 2009 Elsevier B.V. All rights reserved.

Detachment dynamics of colloidal spheres with adhesive interactions

NASA Astrophysics Data System (ADS)

Bergenholtz, J.

2018-04-01

Escape of colloidal-size particles from various kinds of solids, such as aggregates and surfaces, occurs in a wide variety of settings of both fundamental and applied scientific interest. In this paper an exact solution for the detachment of adhesive spheres from each other by means of diffusion is presented. The solution takes into account repeated detachment and reattachment events in the course of time on the way toward the permanently separated state. For strongly adhesive spheres this state is approached in an exponential manner essentially regardless of how the bound state is specified. The analytical solution is shown to capture semiquantitatively the escape from more realistic potential wells using a mapping procedure whereby equality of second virial coefficients is imposed.

Food Safety by Using Machine Learning for Automatic Classification of Seeds of the South-American Incanut Plant

NASA Astrophysics Data System (ADS)

Lemanzyk, Thomas; Anding, Katharina; Linss, Gerhard; Rodriguez Hernández, Jorge; Theska, René

2015-02-01

The following paper deals with the classification of seeds and seed components of the South-American Incanut plant and the modification of a machine to handle this task. Initially the state of the art is being illustrated. The research was executed in Germany and with a relevant part in Peru and Ecuador. Theoretical considerations for the solution of an automatically analysis of the Incanut seeds were specified. The optimization of the analyzing software and the separation unit of the mechanical hardware are carried out with recognition results. In a final step the practical application of the analysis of the Incanut seeds is held on a trial basis and rated on the bases of statistic values.

Automated procedure execution for space vehicle autonomous control

NASA Technical Reports Server (NTRS)

Broten, Thomas A.; Brown, David A.

1990-01-01

Increased operational autonomy and reduced operating costs have become critical design objectives in next-generation NASA and DoD space programs. The objective is to develop a semi-automated system for intelligent spacecraft operations support. The Spacecraft Operations and Anomaly Resolution System (SOARS) is presented as a standardized, model-based architecture for performing High-Level Tasking, Status Monitoring and automated Procedure Execution Control for a variety of spacecraft. The particular focus is on the Procedure Execution Control module. A hierarchical procedure network is proposed as the fundamental means for specifying and representing arbitrary operational procedures. A separate procedure interpreter controls automatic execution of the procedure, taking into account the current status of the spacecraft as maintained in an object-oriented spacecraft model.