Sequence characterization of coding regions of the myostatin gene (GDF8) from Brazilian Murrah buffaloes (Bubalus bubalis) and comparison with the Bos taurus sequence

Within about 30 years the Brazilian buffalo (Bubalus bubalis) herd will reach approximately 50 million head as a result of the great adaptive capacity of these animals to tropical climates, together with the good productive and reproductive potential which make these animals an important animal protein source for poor and developing countries. The myostatin gene (GDF8) is important in the physiology of stock animals because its product produces a direct effect on muscle development and consequently also on meat production. The myostatin sequence is known in several mammalian species and shows a high degree of amino acid sequence conservation, although the presence of non-silent and silent changes in the coding sequences and several alterations in the introns and untranslated regions have been identified. The objective of our work was to characterize the myostatin coding regions of B. bubalis (Murrah breed) and to compare them with the Bos taurus regions looking for variations in nucleotide and protein sequences. In this way, we were able to identify 12 variations at DNA level and five alterations on the presumed myostatin protein sequence as compared to non double-muscled bovine sequences.

Genetic variability of porcine parvovirus isolates revealed by analysis of partial sequences of the structural coding gene VP2

The 3'-terminal 853 nt (and the putative 283 aa) sequence of the VP2-encoding gene from 29 field strains of porcine parvovirus (PPV) were determined and compared both to each other and with other published sequences. Sequences were examined using maximum-parsimony and statistical analyses for nucleotide diversity and sequence variability. Among the nucleotide sequences of the PPV field strains, 26 polymorphic sites were encountered; 22 polymorphic sites were detected in the putative amino acid sequence. Mapping polymorphic sites of protein data onto the three-dimensional (3D) structure of PPV VP2 revealed that almost all substitutions were located on the external surface of the viral capsid. Mapping amino acid substitutions to the alignment between PPV VP2 sequences and the 3D structure of canine parvovirus (CPV) capsid, many PPV substitutions were observed to map to regions of recognized antigenicity and/or to contain phenotypically important residues for CPV and other parvoviruses. In spite of the high sequence similarity, genetic analysis has shown the existence of at least two virus lineages among the samples. In conclusion, these results highlight the need for close surveillance on PPV genetic drift, with an assessment of its potential ability to modify the antigenic make-up of the virus.

On the Baker-Akhiezer function in the AKNS scheme

Expressions for the Baker-Akhiezer function and their logarithmic space and time derivatives are derived in terms of the matrix elements of U - V matrices and 'squared basis functions'. These expressions generalize the well known formulas for the KdV equation case and establish links between different forms of the Whitham averaging procedure.

Extension of the Nambu-Jona-Lasinio model predictions at high densities and temperatures using an implicit regularization scheme

Traditional cutoff regularization schemes of the Nambu-Jona-Lasinio model limit the applicability of the model to energy-momentum scales much below the value of the regularizing cutoff. In particular, the model cannot be used to study quark matter with Fermi momenta larger than the cutoff. In the present work, an extension of the model to high temperatures and densities recently proposed by Casalbuoni, Gatto, Nardulli, and Ruggieri is used in connection with an implicit regularization scheme. This is done by making use of scaling relations of the divergent one-loop integrals that relate these integrals at different energy-momentum scales. Fixing the pion decay constant at the chiral symmetry breaking scale in the vacuum, the scaling relations predict a running coupling constant that decreases as the regularization scale increases, implementing in a schematic way the property of asymptotic freedom of quantum chromodynamics. If the regularization scale is allowed to increase with density and temperature, the coupling will decrease with density and temperature, extending in this way the applicability of the model to high densities and temperatures. These results are obtained without specifying an explicit regularization. As an illustration of the formalism, numerical results are obtained for the finite density and finite temperature quark condensate and applied to the problem of color superconductivity at high quark densities and finite temperature.

A generalized alternating-direction implicit scheme for incompressible magnetohydrodynamic viscous flows at low magnetic Reynolds number

This paper presents numerical simulations of incompressible fluid flows in the presence of a magnetic field at low magnetic Reynolds number. The equations governing the flow are the Navier-Stokes equations of fluid motion coupled with Maxwell's equations of electromagnetics. The study of fluid flows under the influence of a magnetic field and with no free electric charges or electric fields is known as magnetohydrodynamics. The magnetohydrodynamics approximation is considered for the formulation of the non-dimensional problem and for the characterization of similarity parameters. A finite-difference technique is used to discretize the equations. In particular, an extension of the generalized Peaceman and Rachford alternating-direction implicit (ADI) scheme for simulating two-dimensional fluid flows is presented. The discretized conservation equations are solved in stream function-vorticity formulation. We compare the ADI and generalized ADI schemes, and show that the latter is more efficient in simulating low Reynolds number and magnetic Reynolds number problems. Numerical results demonstrating the applicability of this technique are also presented. The simulation of incompressible magneto hydrodynamic fluid flows is illustrated by numerical solution for two-dimensional cases. (c) 2007 Elsevier B.V. All rights reserved.

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

Exact dynamics of single-qubit-gate fidelities under the measurement-based quantum computation scheme

Measurement-based quantum computation is an efficient model to perform universal computation. Nevertheless, theoretical questions have been raised, mainly with respect to realistic noise conditions. In order to shed some light on this issue, we evaluate the exact dynamics of some single-qubit-gate fidelities using the measurement-based quantum computation scheme when the qubits which are used as a resource interact with a common dephasing environment. We report a necessary condition for the fidelity dynamics of a general pure N-qubit state, interacting with this type of error channel, to present an oscillatory behavior, and we show that for the initial canonical cluster state, the fidelity oscillates as a function of time. This state fidelity oscillatory behavior brings significant variations to the values of the computational results of a generic gate acting on that state depending on the instants we choose to apply our set of projective measurements. As we shall see, considering some specific gates that are frequently found in the literature, the fast application of the set of projective measurements does not necessarily imply high gate fidelity, and likewise the slow application thereof does not necessarily imply low gate fidelity. Our condition for the occurrence of the fidelity oscillatory behavior shows that the oscillation presented by the cluster state is due exclusively to its initial geometry. Other states that can be used as resources for measurement-based quantum computation can present the same initial geometrical condition. Therefore, it is very important for the present scheme to know when the fidelity of a particular resource state will oscillate in time and, if this is the case, what are the best times to perform the measurements.

Feynman integrals with tensorial structure in the negative dimensional integration scheme

The negative-dimensional integration method (NDIM) is revealing itself as a very useful technique for computing massless and/or massive Feynman integrals, covariant and noncovanant alike. Up until now however, the illustrative calculations done using such method have been mostly covariant scalar integrals/without numerator factors. We show here how those integrals with tensorial structures also can be handled straightforwardly and easily. However, contrary to the absence of significant features in the usual approach, here the NDIM also allows us to come across surprising unsuspected bonuses. Toward this end, we present two alternative ways of working out the integrals and illustrate them by taking the easiest Feynman integrals in this category that emerge in the computation of a standard one-loop self-energy diagram. One of the novel and heretofore unsuspected bonuses is that there are degeneracies in the way one can express the final result for the referred Feynman integral.

An active leakage-injection scheme applied to low-voltage SRAMs

An active leakage-injection scheme (ALIS) for low-voltage (LV) high-density (HD) SRAMs is presented. By means of a feedback loop comprising a servo-amplifier and a common-drain MOSFET, a current matching the respective bit-line leakage is injected onto the line during precharge and sensing, preventing the respective capacitances from erroneous discharges. The technique is able to handle leakages up to hundreds of μA at high operating temperatures. Since no additional timing is required, read-out operations are performed at no speed penalty. A simplified 256×1bit array was designed in accordance with a 0.35 CMOS process and 1.2V-supply. A range of PSPICE simulation attests the efficacy of ALIS. With an extra power consumption of 242 μW, a 200 μA-leakage @125°C, corresponding to 13.6 times the cell current, is compensated.

Analysis of a sub-optimal scheme of drug dosage in the AIDS treatment

Here the results for CD4+T cells count and the viral load obtained from HIV sero-positive patients are compared with results from numerical simulations by computer. Also, the standard scheme of administration of drugs anti HIV (HAART schemes) which uses constant doses is compared with an alternative sub-optimal teatment scheme which uses variable drug dosage according to the evolution of a quantitative measure of the side effects. The quantitative analysis done here shows that it is possible to obtain, using the alternative scheme, the same performance of actual data but using variable dosage and having fewer side effects. Optimal control theory is used to solve and also to provide a prognosis related to the strategies for control of viraemia.

Gluon mass generation in the PT-BFM scheme

In this article we study the general structure and special properties of the Schwinger-Dyson equation for the gluon propagator constructed with the pinch technique, together with the question of how to obtain infrared finite solutions, associated with the generation of an effective gluon mass. Exploiting the known all-order correspondence between the pinch technique and the background field method, we demonstrate that, contrary to the standard formulation, the non-perturbative gluon self-energy is transverse order-by-order in the dressed loop expansion, and separately for gluonic and ghost contributions. We next present a comprehensive review of several subtle issues relevant to the search of infrared finite solutions, paying particular attention to the role of the seagull graph in enforcing transversality, the necessity of introducing massless poles in the three-gluon vertex, and the incorporation of the correct renormalization group properties. In addition, we present a method for regulating the seagull-type contributions based on dimensional regularization; its applicability depends crucially on the asymptotic behavior of the solutions in the deep ultraviolet, and in particular on the anomalous dimension of the dynamically generated gluon mass. A linearized version of the truncated Schwinger-Dyson equation is derived, using a vertex that satisfies the required Ward identity and contains massless poles belonging to different Lorentz structures. The resulting integral equation is then solved numerically, the infrared and ultraviolet properties of the obtained solutions are examined in detail, and the allowed range for the effective gluon mass is determined. Various open questions and possible connections with different approaches in the literature are discussed. © SISSA 2006.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

Human interferon B1 ser17: Coding DNA synthesis, expression, purification and characterization of bioactive recombinant protein

A protocol to produce large amounts of bioactive homogeneous human interferon β1 expressed in Escherichia coli was developed. Human interferon β1 ser17 gene was constructed, cloned and subcloned, and the recombinant protein expressed in E. coli cells. Solubilization of recombinant human interferon β1 ser17 (rhIFN-β1 ser17) was accomplished by employing a brief shift to high alkaline pH in the presence of non-ionic detergent. The recombinant protein was purifi ed by three chromatographic steps. N-terminal amino acid sequencing and mass spectrometry analysis provided experimental evidence for the identity of the recombinant protein. Reverse phase liquid chromatography demonstrated that the content of deamidates and sulphoxides was similar to a commercial standard. Size exclusion chromatography demonstrated the absence of high molecular mass aggregates and dimers. The protocol represents an effi cient and high-yield method to obtain bioactive homogeneous monomeric rhIFN-β1 ser17 protein. It may thus represent an important step towards scaling up for rhIFN-β1 ser17 large-scale production. © 2010 Villela AD, et al.

Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs

Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we present a quantitative analysis of the gene content from publicly available sugarcane ESTs. The current sugarcane EST collection sampled orthologs for ~58 % of the closely-related sorghum proteome, suggesting that more than 10,000 sugarcane coding-genes remain undiscovered. Moreover the existence of more than 2,000 ncRNAs conserved between sugarcane and sorghum was revealed, among which over 500 are also detected in rice, supporting the existence of hundreds of conserved ncRNAs in grasses. New efforts towards sugarcane transcriptome sequencing were needed to sample the missing coding-genes as well as to expand the catalog of ncRNAs. © 2012 Springer Science+Business Media, LLC.

Application of a bounded upwinding scheme to complex fluid dynamics problems

This paper is concerned with an overview of upwinding schemes, and further nonlinear applications of a recently introduced high resolution upwind differencing scheme, namely the ADBQUICKEST [V.G. Ferreira, F.A. Kurokawa, R.A.B. Queiroz, M.K. Kaibara, C.M. Oishi, J.A.Cuminato, A.F. Castelo, M.F. Tomé, S. McKee, assessment of a high-order finite difference upwind scheme for the simulation of convection-diffusion problems, International Journal for Numerical Methods in Fluids 60 (2009) 1-26]. The ADBQUICKEST scheme is a new TVD version of the QUICKEST [B.P. Leonard, A stable and accurate convective modeling procedure based on quadratic upstream interpolation, Computer Methods in Applied Mechanics and Engineering 19 (1979) 59-98] for solving nonlinear balance laws. The scheme is based on the concept of NV and TVD formalisms and satisfies a convective boundedness criterion. The accuracy of the scheme is compared with other popularly used convective upwinding schemes (see, for example, Roe (1985) [19], Van Leer (1974) [18] and Arora & Roe (1997) [17]) for solving nonlinear conservation laws (for example, Buckley-Leverett, shallow water and Euler equations). The ADBQUICKEST scheme is then used to solve six types of fluid flow problems of increasing complexity: namely, 2D aerosol filtration by fibrous filters; axisymmetric flow in a tubular membrane; 2D two-phase flow in a fluidized bed; 2D compressible Orszag-Tang MHD vortex; axisymmetric jet onto a flat surface at low Reynolds number and full 3D incompressible flows involving moving free surfaces. The numerical simulations indicate that this convective upwinding scheme is a good generic alternative for solving complex fluid dynamics problems. © 2012.