A eubacterial origin for the human tRNA nucleotidyltransferase?

tRNA CCA-termini are generated and maintained by tRNA nucleotidyltransferases. Together with poly(A) polymerases and other enzymes they belong to the nucleotidyltransferase superfamily. However, sequence alignments within this family do not allow to distinguish between CCA-adding enzymes and poly(A) polymerases. Furthermore, due to the lack of sequence information about animal CCA-adding enzymes, identification of corresponding animal genes was not possible so far. Therefore, we looked for the human homolog using the baker's yeast tRNA nucleotidyltransferase as a query sequence in a BLAST search. This revealed that the human gene transcript CGI-47, (\#AF151805) deposited in GenBank is likely to encode such an enzyme. To identify the nature of this protein, the cDNA of the transcript was cloned and the recombinant protein biochemically characterized, indicating that CGI-47 encodes a bona fide CCA-adding enzyme and not a poly(A) polymerase. This confirmed animal CCA-adding enzyme allowed us to identify putative homologs from other animals. Calculation of a neighbor-joining tree, using an alignment of several CCA-adding enzymes, revealed that the animal enzymes resemble more eubacterial ones than eukaryotic plant and fungal tRNA nucleotidyltransferases, suggesting that the animal nuclear cca genes might have been derived from the endosymbiotic progenitor of mitochondria and are therefore of eubacterial origin

Business Cycle Asymmetries: Characterisationand Testing Based on Markov-Switching Autoregression.

We propose testing for business cycle asymmetries in Markov-switching autoregressive (MS-AR) models. We derive the parametric restrictions on MS-AR models that rule out types of asymmetries such as deepness, steepness, and sharpness, and set out a testing procedure based on Wald statistics which have standard asymptotic. For a two-regime model, such as that popularized by Hamilton (1989), we show that deepness implies sharpness (and vice versa) while the process is always non-steep. We illustrate with two and three-state MS models of US GNP growth, and with models of US output and employment. Our findings are compared with those obtained from standard non-parametric tests.BUSINESS CYCLES ; TESTS

Plausible families of compact objects with a Non Local Equation of State

We investigate the plausibility of some models emerging from an algorithm devised to generate a one-parameter family of interior solutions for the Einstein equations. It is explored how their physical variables change as the family-parameter varies. The models studied correspond to anisotropic spherical matter configurations having a non local equation of state. This particular type of equation of state with no causality problems provides, at a given point, the radial pressure not only as a function of the density but as a functional of the enclosed matter distribution. We have found that there are several model-independent tendencies as the parameter increases: the equation of state tends to be stiffer and the total mass becomes half of its external radius. Profiting from the concept of cracking of materials in General Relativity, we obtain that those models become more stable as the family parameter increases

Singularity, complexity, and quasi--integrability of rational mappings

We investigate global properties of the mappings entering the description of symmetries of integrable spin and vertex models, by exploiting their nature of birational transformations of projective spaces. We give an algorithmic analysis of the structure of invariants of such mappings. We discuss some characteristic conditions for their (quasi)--integrability, and in particular its links with their singularities (in the 2--plane). Finally, we describe some of their properties {\it qua\/} dynamical systems, making contact with Arnol'd's notion of complexity, and exemplify remarkable behaviours.Comment: Latex file. 17 pages. To appear in CM

The interaction of amyloid A beta(1-40) with lipid bilayers and ganglioside as studied by P-31 solid-state NMR

Amyloid P-peptide (A beta) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate fro m regions of neuronal membrane rich in gangliosides. We analyzed the mode of interaction of A beta with lipid bilayers by multinuclear NMR using P-31 nuclei. We found that A beta (1-40) strongly perturbed the bilayer structure of dimyristoylphosphatidylcholine (DMPQ, to form a non-lamellar phase (most likely micellar). The ganglioside GM1 potentiated the effect of A beta (1-40), as viewed from P-31 NMR. The difference of the isotropic peak intensity between DMPC/A beta and DMPC/GM1/A beta suggests a specific interaction between A beta and GM1. We show that in the DMPC/GM1/A beta system there are three lipid phases, namely a lamellar phase, a hexagonal phase and non-oriented lipids. The latter two phases are induced by the presence of the A beta peptide, and facilitated by GM1. 9) 2008 Elsevier Ireland Ltd. All rights reserved

Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales

Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple introductions of WSSV occurred in central Vietnam, it is largely uncertain how WSSV was introduced and subsequently spread. Here, we evaluate five variable WSSV DNA loci as markers of virus spread on an intermediate (i.e. regional) scale, and develop a detailed and statistically supported model for the spread of WSSV. The genotypes of 17 WSSV isolates from along the coast of Vietnam – nine of which were newly characterized in this study – were analysed to obtain sufficient samples on an intermediate scale and to allow statistical analysis. Only the ORF23/24 variable region is an appropriate marker on this scale, as geographically proximate isolates show similar deletion sizes. The ORF14/15 variable region and variable-number tandem repeat (VNTR) loci are not useful as markers on this scale. ORF14/15 may be suitable for studying larger spatiotemporal scales, whereas VNTR loci are probably suitable for smaller scales. For ORF23/24, there is a clear pattern in the spatial distribution of WSSV: the smallest genomic deletions are found in central Vietnam, and larger deletions are found in the south and the north. WSSV genomic deletions tend to increase over time with virus spread in cultured shrimp, and our data are therefore congruent with the hypothesis that WSSV was introduced in central Vietnam and then radiated ou

Universal and unique features of kinesin motors: Insights from a comparison of fungal and animal conventional kinesins

Kinesins are microtubule motors that use the energy derived from the hydrolysis of ATP to move unidirectionally along microtubules, The founding member of this still growing superfamily is conventional kinesin, a dimeric motor that moves processively towards the plus end of microtubules, Within the family of conventional kinesins, two groups can be distinguished to date, one derived from animal species, and one originating from filamentous fungi. So far no conventional kinesin has been reported from plant cells. Fungal and animal conventional kinesins differ in several respects, both in terms of their primary sequence and their physiological properties. Thus all fungal conventional kinesins move at velocities that are 4-5 times higher than those of animal conventional kinesins, and all of them appear to lack associated light chains. Both groups of motors are characterized by a number of group-specific sequence features which are considered here with respect to their functional importance. Animal and fungal conventional kinesins also share a number of sequence characteristics which point to common principles of motor function. The overall domain organization is remarkably similar. A C-terminal sequence motif common to all kinesins, which constitutes the only region of high homology outside the motor domain, suggests common principles of cargo association in both groups of motors. Consideration of the differences of, and similarities between, fungal and animal kinesins offers novel possibilities for experimentation (e.g., by constructing chimeras) that can be expected to contribute to our understanding of motor function

Polarization phenomena in open charm photoproduction processes

We analyze polarization effects in associative photoproduction of pseudoscalar ($\bar{D}$) charmed mesons in exclusive processes $\gamma+ N\to Y_c +\bar{D}$, $Y_c=\Lambda_c^+$, $\Sigma_c$. Circularly polarized photons induce nonzero polarization of the $Y_c$-hyperon with $x$- and $z$-components (in the reaction plane) and non vanishing asymmetries ${\cal A}_x$ and ${\cal A}_z$ for polarized nucleon target. These polarization observables can be predicted in model-independent way for exclusive $\bar{D}$-production processes in collinear kinematics. The T-even $Y_c$-polarization and asymmetries for non-collinear kinematics can be calculated in framework of an effective Lagrangian approach. The depolarization coefficients $D_{ab}$, characterizing the dependence of the $Y_c$-polarization on the nucleon polarization are also calculated.Comment: 36 pages 13 figure

Risk factors for chest infection in acute stroke: a prospective cohort study

<p><b>Background and Purpose:</b> Pneumonia is a major cause of morbidity and mortality after stroke. We aimed to determine key characteristics that would allow prediction of those patients who are at highest risk for poststroke pneumonia.</p> <p><b>Methods:</b> We studied a series of consecutive patients with acute stroke who were admitted to hospital. Detailed evaluation included the modified National Institutes of Health Stroke Scale; the Abbreviated Mental Test; and measures of swallow, respiratory, and oral health status. Pneumonia was diagnosed by set criteria. Patients were followed up at 3 months after stroke.</p> <p><b>Results:</b> We studied 412 patients, 391 (94.9%) with ischemic stroke and 21 (5.1%) with hemorrhagic stroke; 78 (18.9%) met the study criteria for pneumonia. Subjects who developed pneumonia were older (mean±SD age, 75.9±11.4 vs 64.9±13.9 years), had higher modified National Institutes of Health Stroke Scale scores, a history of chronic obstructive pulmonary disease, lower Abbreviated Mental Test scores, and a higher oral cavity score, and a greater proportion tested positive for bacterial cultures from oral swabs. In binary logistic-regression analysis, independent predictors (P<0.05) of pneumonia were age >65 years, dysarthria or no speech due to aphasia, a modified Rankin Scale score ≥4, an Abbreviated Mental Test score <8, and failure on the water swallow test. The presence of 2 or more of these risk factors carried 90.9% sensitivity and 75.6% specificity for the development of pneumonia.</p> <p><b>Conclusions:</b> Pneumonia after stroke is associated with older age, dysarthria/no speech due to aphasia, severity of poststroke disability, cognitive impairment, and an abnormal water swallow test result. Simple assessment of these variables could be used to identify patients at high risk of developing pneumonia after stroke.</p&gt

Transfer-Matrix Monte Carlo Estimates of Critical Points in the Simple Cubic Ising, Planar and Heisenberg Models

The principle and the efficiency of the Monte Carlo transfer-matrix algorithm are discussed. Enhancements of this algorithm are illustrated by applications to several phase transitions in lattice spin models. We demonstrate how the statistical noise can be reduced considerably by a similarity transformation of the transfer matrix using a variational estimate of its leading eigenvector, in analogy with a common practice in various quantum Monte Carlo techniques. Here we take the two-dimensional coupled $XY$-Ising model as an example. Furthermore, we calculate interface free energies of finite three-dimensional O($n$) models, for the three cases $n=1$, 2 and 3. Application of finite-size scaling to the numerical results yields estimates of the critical points of these three models. The statistical precision of the estimates is satisfactory for the modest amount of computer time spent