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Search Results: 1 - 10 of 244745 matches for " Paul R Copeland "
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Making sense of nonsense: the evolution of selenocysteine usage in proteins
Paul R Copeland
Genome Biology , 2005, DOI: 10.1186/gb-2005-6-6-221
Abstract: As well as the 20 amino acids universally found in proteins, two other amino acids - pyrrolysine and selenocysteine - are incorporated into a small number of proteins in some groups of organisms. L-pyrrolysine is a C4-substituted pyrroline-5-carboxylate attached to the ε-nitrogen of lysine; L-seleno-cysteine is identical to cysteine but with selenium substituted for sulfur. Pyrrolysine has so far been found only in enzymes required for methanogenesis in some archaebacteria, suggesting a possible role in catalysis, but the precise role of this amino acid has not been identified. The selenium atom in selenocysteine confers a much higher reactivity than cysteine, as its lower pKa (5.2) allows it to remain ionized at physiological pH. Most selenoproteins use their higher nucleophilic activity to catalyze redox reactions, but many have no known function. The current studies of selenoprotein evolution represent one of the important tools used to completely identify and categorize selenoprotein function.The Sargasso Sea (named for the surface-borne sargassum seaweed) is a body of water covering 2 million square miles in the middle of the North Atlantic Ocean near Bermuda. Its well defined physical and geochemical properties, including relatively low nutrient levels, made it an alluring target for a shotgun sequencing project covering a whole biome - a collection of interrelated ecosystems typical of a particular physical environment [1]. This effort, the first 'biome sequencing project', represents a novel application for shotgun genome sequencing and is an important new component of modern bioinformatics. Of the 1.2 million genes identified by this approach, however, a small subset is likely to be misannotated because of the presence of in-frame nonsense codons, either UGA or UAG, which in these cases are acting as codons for selenocysteine and pyrrolysine, respectively. In some archaea, the UAG codon is redefined as a pyrrolysine codon, apparently forcing these organisms
Selenocysteine Insertion Sequence Binding Protein 2L Is Implicated as a Novel Post-Transcriptional Regulator of Selenoprotein Expression
Jesse Donovan, Paul R. Copeland
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035581
Abstract: The amino acid selenocysteine (Sec) is encoded by UGA codons. Recoding of UGA from stop to Sec requires a Sec insertion sequence (SECIS) element in the 3′ UTR of selenoprotein mRNAs. SECIS binding protein 2 (SBP2) binds the SECIS element and is essential for Sec incorporation into the nascent peptide. SBP2-like (SBP2L) is a paralogue of SBP2 in vertebrates and is the only SECIS binding protein in some invertebrates where it likely directs Sec incorporation. However, vertebrate SBP2L does not promote Sec incorporation in in vitro assays. Here we present a comparative analysis of SBP2 and SBP2L SECIS binding properties and demonstrate that its inability to promote Sec incorporation is not due to lower SECIS affinity but likely due to lack of a SECIS dependent domain association that is found in SBP2. Interestingly, however, we find that an invertebrate version of SBP2L is fully competent for Sec incorporation in vitro. Additionally, we present the first evidence that SBP2L interacts with selenoprotein mRNAs in mammalian cells, thereby implying a role in selenoprotein expression.
Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins
Jesse Donovan, Paul R Copeland
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-229
Abstract: In this report we present a phylogeny of the eukaryotic SECIS binding protein family which includes SBP2 and a related protein we herein term SBP2L. Here we show that SBP2L is an SBP2 paralogue in vertebrates and is the only form of SECIS binding protein in invertebrate deuterostomes, suggesting a key role in Sec incorporation in these organisms, but an SBP2/SBP2L fusion protein is unable to support Sec incorporation in vitro. An in-depth phylogenetic analysis of the conserved L7Ae RNA binding domain suggests an ancestral relationship with ribosomal protein L30. In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5.Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages. In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.All domains of life possess the ability to recode select UGA codons from a translation termination signal to a selenocysteine (Sec) codon. The translation products of successful Sec incorporation are termed selenoproteins. In eukaryotes the recognition of UGA as a Sec codon by the protein synthetic machinery requires a cis-acting Sec insertion sequence (SECIS) element in the 3' untranslated regions (UTRs) of selenoprotein mRNAs. Eukaryotic SECIS elements are stable stem-loop structures that are comprised of two helices separated by a kink-turn containing a conserved GA quartet (SECIS core) and an apical AAR motif that is present either as a terminal loop (Form 1) or a terminal bulge (Form 2) [reviewed in [1]]. The trans-acting factors known to be required for Sec incorporation are SECIS binding protein 2 (SBP2), Sec-tRNASec, and the Sec specific translation elongation factor, eEFSec. SBP2 is the most studied of the known trans-acting eukaryotic Sec incorporation factors. Structure/funct
World Federation for Mental Health perspectives on person-centered medicine
John R.M. Copeland
International Journal of Integrated Care , 2010,
Abstract:
Cosmological perturbations and the transition from contraction to expansion
C. Cartier,R. Durrer,E. J. Copeland
Physics , 2003, DOI: 10.1103/PhysRevD.67.103517
Abstract: We investigate both analytically and numerically the evolution of scalar perturbations generated in models which exhibit a smooth transition from a contracting to an expanding Friedmann universe. We find that the resulting spectral index in the late radiation dominated universe depends on which of the $\Psi$ or \$zeta$ variables passes regularly through the transition. The results can be parameterized through the exponent $q$ defining the rate of contraction of the universe. For $q \geq -1/2$ we find that there are no stable cases where both variables are regular during the transition. In particular, for $0
The graceful exit in pre-big bang string cosmology
C. Cartier,E. J. Copeland,R. Madden
Physics , 1999, DOI: 10.1088/1126-6708/2000/01/035
Abstract: We re-examine the graceful exit problem in the pre-big bang scenario of string cosmology, by considering the most general time-dependent classical correction to the Lagrangian with up to four derivatives. By including possible forms for quantum loop corrections we examine the allowed region of parameter space for the coupling constants which enable our solutions to link smoothly the two asymptotic low-energy branches of the pre-big bang scenario, and observe that these solutions can satisfy recently proposed entropic bounds on viable singularity free cosmologies.
Identification of the Boudicca and Sinbad retrotransposons in the genome of the human blood fluke Schistosoma haematobium
Copeland, Claudia S;Lewis, Fred A;Brindley, Paul J;
Memórias do Instituto Oswaldo Cruz , 2006, DOI: 10.1590/S0074-02762006000500015
Abstract: schistosomes have a comparatively large genome, estimated for schistosoma mansoni to be about 270 megabase pairs (haploid genome). recent findings have shown that mobile genetic elements constitute significant proportions of the genomes of s. mansoni and s. japonicum. much less information is available on the genome of the third major human schistosome, s. haematobium. in order to investigate the possible evolutionary origins of the s. mansoni long terminal repeat retrotransposons boudicca and sinbad, several genomes were searched by southern blot for the presence of these retrotransposons. these included three species of schistosomes, s. mansoni, s. japonicum, and s. haematobium, and three related platyhelminth genomes, the liver flukes fasciola hepatica and fascioloides magna and the planarian, dugesia dorotocephala. in addition, homo sapiens and three snail host genomes, biomphalaria glabrata, oncomelania hupensis, and bulinus truncatus, were examined for possible indications of a horizontal origin for these retrotransposons. southern hybridization analysis indicated that both boudicca and sinbad were present in the genome of s. haematobium. furthermore, low stringency southern hybridization analyses suggested that a boudicca-like retrotransposon was present in the genome of b. truncatus, the snail host of s. haematobium.
General second order scalar-tensor theory, self tuning, and the Fab Four
Christos Charmousis,Edmund J. Copeland,Antonio Padilla,Paul M. Saffin
Physics , 2011, DOI: 10.1103/PhysRevLett.108.051101
Abstract: Starting from the most general scalar-tensor theory with second order field equations in four dimensions, we establish the unique action that will allow for the existence of a consistent self-tuning mechanism on FLRW backgrounds, and show how it can be understood as a combination of just four base Lagrangians with an intriguing geometric structure dependent on the Ricci scalar, the Einstein tensor, the double dual of the Riemann tensor and the Gauss-Bonnet combination. Spacetime curvature can be screened from the net cosmological constant at any given moment because we allow the scalar field to break Poincar\'e invariance on the self-tuning vacua, thereby evading the Weinberg no-go theorem. We show how the four arbitrary functions of the scalar field combine in an elegant way opening up the possibility of obtaining non-trivial cosmological solutions.
Cosmological Constraints on $f(G)$ Dark Energy Models
Shuang-Yong Zhou,Edmund J. Copeland,Paul M. Saffin
Physics , 2009, DOI: 10.1088/1475-7516/2009/07/009
Abstract: Modified gravity theories with the Gauss-Bonnet term $G=R^2-4R^{\mu\nu}R_{\mu\nu}+R^{\mu\nu\rho\sigma}R_{\mu\nu\rho\sigma}$ have recently gained a lot of attention as a possible explanation of dark energy. We perform a thorough phase space analysis on the so-called $f(G)$ models, where $f(G)$ is some general function of the Gauss-Bonnet term, and derive conditions for the cosmological viability of $f(G)$ dark energy models. Following the $f(R)$ case, we show that these conditions can be nicely presented as geometrical constraints on the derivatives of $f(G)$. We find that for general $f(G)$ models there are two kinds of stable accelerated solutions, a de Sitter solution and a phantom-like solution. They co-exist with each other and which solution the universe evolves to depends on the initial conditions. Finally, several toy models of $f(G)$ dark energy are explored. Cosmologically viable trajectories that mimic the $\Lambda$CDM model in the radiation and matter dominated periods, but have distinctive signatures at late times, are obtained.
Charge-Swapping Q-balls
Edmund J. Copeland,Paul M. Saffin,Shuang-Yong Zhou
Physics , 2014, DOI: 10.1103/PhysRevLett.113.231603
Abstract: Q-balls are non-topological solitonic solutions to a wide class of field theories that possess global symmetries. Here we show that in these same theories there also exists a tower of novel composite Q-ball solutions where, within one composite Q-ball, positive and negative charges co-exist and swap at a frequency lower than the natural frequency of an individual Q-ball. These charge-swapping Q-balls are constructed by assembling Q-balls and anti-Q-balls tightly such that their nonlinear cores overlap. We explain why charge-swapping Q-balls can form and why they swap charges.
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