Overexpression of the Rv0805 phosphodiesterase elicits a cAMP-independent transcriptional response

The Rv0805 gene in Mycobacterium tuberculosis encodes a metallophosphoesterase which shows cAMP-hydrolytic activity. Overexpression of Rv0805 has been used as a tool to lower intracellular cAMP levels and thereby elucidate the roles of cAMP in mycobacteria. Here we show that levels of cAMP in M. tuberculosis were lowered by only similar to 30% following overexpression of Rv0805, and transcript levels of a number of genes, which include those associated with virulence and the methyl citrate cycle, were altered. The genes that showed altered expression were distinct from those differentially regulated in a strain deleted for the cAMP-receptor protein (CRPMt), consistent with the relatively low dependence on cAMP of CRPMt binding to DNA. Using mutants of Rv0805 we show that the transcriptional signature of Rv0805 overexpression is a combination of catalysis-dependent and independent effects, and that the structurally flexible C-terminus of Rv0805 is crucial for the catalysis-independent effects of the protein. Our study demonstrates the dissociation of Rv0805 and cAMP-regulated gene expression, and reveals alternate functions for this phosphodiesterase from M. tuberculosis.

Partial delamination modeling in composite beams using a finite element method

A new method of modeling partial delamination in composite beams is proposed and implemented using the finite element method. Homogenized cross-sectional stiffness of the delaminated beam is obtained by the proposed analytical technique, including extension-bending, extension-twist and torsion-bending coupling terms, and hence can be used with an existing finite element method. A two noded C1 type Timoshenko beam element with 4 degrees of freedom per node for dynamic analysis of beams is implemented. The results for different delamination scenarios and beams subjected to different boundary conditions are validated with available experimental results in the literature and/or with the 3D finite element simulation using COMSOL. Results of the first torsional mode frequency for the partially delaminated beam are validated with the COMSOL results. The key point of the proposed model is that partial delamination in beams can be analyzed using a beam model, rather than using 3D or plate models. (c) 2013 Elsevier B.V. All rights reserved.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, first a Fortran code is developed for three dimensional linear elastostatics using constant boundary elements; the code is based on a MATLAB code developed by the author earlier. Next, the code is parallelized using BLACS, MPI, and ScaLAPACK. Later, the parallelized code is used to demonstrate the usefulness of the Boundary Element Method (BEM) as applied to the realtime computational simulation of biological organs, while focusing on the speed and accuracy offered by BEM. A computer cluster is used in this part of the work. The commercial software package ANSYS is used to obtain the `exact' solution against which the solution from BEM is compared; analytical solutions, wherever available, are also used to establish the accuracy of BEM. A pig liver is the biological organ considered. Next, instead of the computer cluster, a Graphics Processing Unit (GPU) is used as the parallel hardware. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature. Also, a serial MATLAB code, and both serial and parallel versions of a Fortran code, which can solve three dimensional (3D) linear elastostatic problems using constant boundary elements, are provided as supplementary files that can be freely downloaded.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated, with specific reference to the speed and the accuracy offered by BEM. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. A pig liver is the biological organ considered. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

IRES mediated translational regulation of p53 isoforms

p53 is a well known tumor suppressor protein that plays a critical role in cell cycle arrest and apoptosis. It has several isoforms which are produced by transcriptional and posttranscriptional regulatory mechanisms. p53 mRNA has been demonstrated to be translated into two isoforms, full-length p53 (FL-p53) and a truncated isoform N-p53 by the use of alternative translation initiation sites. The mechanism of translation regulation of these two isoforms was further elucidated by the discovery of IRES elements in the p53 mRNA. These two IRESs were shown to regulate the translation of p53 and N-p53 in a distinct cell-cycle phase-dependent manner. This review focuses on the current understanding of the regulation of p53 IRES mediated translation and the role of cis and trans acting factors that influence expression of p53 isoforms. (C) 2013 John Wiley & Sons, Ltd.

Modulation of redox regulatory molecules and electron transport chain activity in muscle of air breathing fish Heteropneustes fossilis under air exposure stress

Responses of redox regulatory system to long-term survival (> 18 h) of the catfish Heteropneustes fossilis in air are not yet understood. Lipid and protein oxidation level, oxidant (H2O2) generation, antioxidative status (levels of superoxide dismutase, catalase, glutathione peroxidase and reductase, ascorbic acid and non-protein sulfhydryl) and activities of respiratory complexes (I, II, III and IV) in mitochondria were investigated in muscle of H. fossilis under air exposure condition (0, 3, 6, 12 and 18 h at 25 A degrees C). The increased levels of both H2O2 and tissue oxidation were observed due to the decreased activities of antioxidant enzymes in muscle under water deprivation condition. However, ascorbic acid and non-protein thiol groups were the highest at 18 h air exposure time. A linear increase in complex II activity with air exposure time and an increase up to 12 h followed by a decrease in activity of complex I at 18 h were observed. Negative correlation was observed for complex III and V activity with exposure time. Critical time to modulate the above parameters was found to be 3 h air exposure. Dehydration induced oxidative stress due to modulation of electron transport chain and redox metabolizing enzymes in muscle of H. fossilis was clearly observed. Possible contribution of redox regulatory system in muscle tissue of the fish for long-term survival in air is elucidated. Results of the present study may be useful to understand the redox metabolism in muscle of fishes those are exposed to air in general and air breathing fishes in particular.

A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

Co-evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria

The transcription from rrn and a number of other promoters is regulated by initiating ribonucleotides (iNTPs) and guanosine tetra/penta phosphate (p)ppGpp], either by strengthening or by weakening of the RNA polymerase (RNAP)-promoter interactions during initiation. Studies in Escherichia coli revealed the importance of a sequence termed discriminator, located between -10 and the transcription start site of the responsive promoters in this mode of regulation. Instability of the open complex at these promoters is attributed to the lack of stabilizing interactions between the suboptimal discriminator and the 1.2 region of sigma 70 (Sig70) in RNAP holoenzyme. We demonstrate a different pattern of interaction between the promoters and sigma A (SigA) of Mycobacterium tuberculosis to execute similar regulation. Instead of cytosine and methionine, thymine at three nucleotides downstream to -10 element and leucine 232 in SigA are found to be essential for iNTPs and pppGpp mediated response at the rrn and gyr promoters of the organism. The specificity of the interaction is substantiated by mutational replacements, either in the discriminator or in SigA, which abolish the nucleotide mediated regulation in vitro or in vivo. Specific yet distinct bases and the amino acids appear to have co-evolved' to retain the discriminator-sigma 1.2 region regulatory switch operated by iNTPs/pppGpp during the transcription initiation in different bacteria.

Prediction of the stiffness of nanoclay-polypropylene composites using a monte carlo finite element analysis approach

The present work deals with the prediction of stiffness of an Indian nanoclay-reinforced polypropylene composite (that can be termed as a nanocomposite) using a Monte Carlo finite element analysis (FEA) technique. Nanocomposite samples are at first prepared in the laboratory using a torque rheometer for achieving desirable dispersion of nanoclay during master batch preparation followed up with extrusion for the fabrication of tensile test dog-bone specimens. It has been observed through SEM (scanning electron microscopy) images of the prepared nanocomposite containing a given percentage (3–9% by weight) of the considered nanoclay that nanoclay platelets tend to remain in clusters. By ascertaining the average size of these nanoclay clusters from the images mentioned, a planar finite element model is created in which nanoclay groups and polymer matrix are modeled as separate entities assuming a given homogeneous distribution of the nanoclay clusters. Using a Monte Carlo simulation procedure, the distribution of nanoclay is varied randomly in an automated manner in a commercial FEA code, and virtual tensile tests are performed for computing the linear stiffness for each case. Values of computed stiffness modulus of highest frequency for nanocomposites with different nanoclay contents correspond well with the experimentally obtained measures of stiffness establishing the effectiveness of the present approach for further applications.

The translation initiation factor DAP5 promotes IRES-driven translation of p53 mRNA

Translational regulation of the p53 mRNA can determine the ratio between p53 and its N-terminal truncated isoforms and therefore has a significant role in determining p53-regulated signaling pathways. Although its importance in cell fate decisions has been demonstrated repeatedly, little is known about the regulatory mechanisms that determine this ratio. Two internal ribosome entry sites (IRESs) residing within the 5'UTR and the coding sequence of p53 mRNA drive the translation of full-length p53 and Delta 40p53 isoform, respectively. Here, we report that DAP5, a translation initiation factor shown to positively regulate the translation of various IRES containing mRNAs, promotes IRES-driven translation of p53 mRNA. Upon DAP5 depletion, p53 and Delta 40p53 protein levels were decreased, with a greater effect on the N-terminal truncated isoform. Functional analysis using bicistronic vectors driving the expression of a reporter gene from each of these two IRESs indicated that DAP5 preferentially promotes translation from the second IRES residing in the coding sequence. Furthermore, p53 mRNA expressed from a plasmid carrying this second IRES was selectively shifted to lighter polysomes upon DAP5 knockdown. Consequently, Delta 40p53 protein levels and the subsequent transcriptional activation of the 14-3-3 sigma gene, a known target of Delta 40p53, were strongly reduced. In addition, we show here that DAP5 interacts with p53 IRES elements in in vitro and in vivo binding studies, proving for the first time that DAP5 directly binds a target mRNA. Thus, through its ability to regulate IRES-dependent translation of the p53 mRNA, DAP5 may control the ratio between different p53 isoforms encoded by a single mRNA.

A finite element method for the Saint-Venant torsion and bending problems for prismatic beams

In this work, we present a finite element formulation for the Saint-Venant torsion and bending problems for prismatic beams. The torsion problem formulation is based on the warping function, and can handle multiply-connected regions (including thin-walled structures), compound and anisotropic bars. Similarly, the bending formulation, which is based on linearized elasticity theory, can handle multiply-connected domains including thin-walled sections. The torsional rigidity and shear centers can be found as special cases of these formulations. Numerical results are presented to show the good coarse-mesh accuracy of both the formulations for both the displacement and stress fields. The stiffness matrices and load vectors (which are similar to those for a variable body force in a conventional structural mechanics problem) in both formulations involve only domain integrals, which makes them simple to implement and computationally efficient. (C) 2014 Elsevier Ltd. All rights reserved.

Spectral finite element based on an efficient layerwise theory for wave propagation analysis of composite and sandwich beams

In this paper, we present a spectral finite element model (SFEM) using an efficient and accurate layerwise (zigzag) theory, which is applicable for wave propagation analysis of highly inhomogeneous laminated composite and sandwich beams. The theory assumes a layerwise linear variation superimposed with a global third-order variation across the thickness for the axial displacement. The conditions of zero transverse shear stress at the top and bottom and its continuity at the layer interfaces are subsequently enforced to make the number of primary unknowns independent of the number of layers, thereby making the theory as efficient as the first-order shear deformation theory (FSDT). The spectral element developed is validated by comparing the present results with those available in the literature. A comparison of the natural frequencies of simply supported composite and sandwich beams obtained by the present spectral element with the exact two-dimensional elasticity and FSDT solutions reveals that the FSDT yields highly inaccurate results for the inhomogeneous sandwich beams and thick composite beams, whereas the present element based on the zigzag theory agrees very well with the exact elasticity solution for both thick and thin, composite and sandwich beams. A significant deviation in the dispersion relations obtained using the accurate zigzag theory and the FSDT is also observed for composite beams at high frequencies. It is shown that the pure shear rotation mode remains always evanescent, contrary to what has been reported earlier. The SFEM is subsequently used to study wavenumber dispersion, free vibration and wave propagation time history in soft-core sandwich beams with composite faces for the first time in the literature. (C) 2014 Elsevier Ltd. All rights reserved.

In the Sense of Transcription Regulation by G-Quadruplexes: Asymmetric Effects in Sense and Antisense Strands

G-Quadruplexes occupy important regulatory regions in the genome. DNA G-quadruplexes in the promoter regions and RNA quadruplexes in the UTRs (untranslated regions) have been individually studied and variously implicated at different regulatory levels of gene expression. However, the formation of G-quadruplexes in the sense and antisense strands and their corresponding roles in gene regulation have not been studied in much detail. In the present study, we have elucidated the effect of strand asymmetry in this context. Using biophysical methods, we have demonstrated the formation of stable G-quadruplex structure in vitro using CD and UV melting. Additionally, ITC was employed to demonstrate that a previously reported selective G-quadruplex ligand was able to bind and stabilize the G-quadruplex in the present sequence. Further, we have shown using reporter constructs that although the DNA G-quadruplex in either strand can reduce translation efficiency, transcriptional regulation differs when G-quadruplex is present in the sense or antisense strand. We demonstrate that the G-quadruplex motif in the antisense strand substantially inhibits transcription, while when in the sense strand, it does not affect transcription, although it does ultimately reduce translation. Further, it is also shown that the G-quadruplex stabilizing ligand can enhance this asymmetric transcription regulation as a result of the increased stabilization of the G-quadruplex.

An extended finite element model coupled with level set method for stable pitting corrosion

Mass balance between metal and electrolytic solution, separated by a moving interface, in stable pit growth results in a set of governing equations which are solved for concentration field and interface position (pit boundary evolution), which requires only three inputs, namely the solid metal concentration, saturation concentration of the dissolved metal ions and diffusion coefficient. A combined eXtended Finite Element Model (XFEM) and level set method is developed in this paper. The extended finite element model handles the jump discontinuity in the metal concentrations at the interface, by using discontinuous-derivative enrichment formulation for concentration discontinuity at the interface. This eliminates the requirement of using front conforming mesh and re-meshing after each time step as in conventional finite element method. A numerical technique known as level set method tracks the position of the moving interface and updates it over time. Numerical analysis for pitting corrosion of stainless steel 304 is presented. The above proposed method is validated by comparing the numerical results with experimental results, exact solutions and some other approximate solutions.

Automatic finite element formulation and assembly of hyperelastic higher order structural models

The formulation of higher order structural models and their discretization using the finite element method is difficult owing to their complexity, especially in the presence of non-linearities. In this work a new algorithm for automating the formulation and assembly of hyperelastic higher-order structural finite elements is developed. A hierarchic series of kinematic models is proposed for modeling structures with special geometries and the algorithm is formulated to automate the study of this class of higher order structural models. The algorithm developed in this work sidesteps the need for an explicit derivation of the governing equations for the individual kinematic modes. Using a novel procedure involving a nodal degree-of-freedom based automatic assembly algorithm, automatic differentiation and higher dimensional quadrature, the relevant finite element matrices are directly computed from the variational statement of elasticity and the higher order kinematic model. Another significant feature of the proposed algorithm is that natural boundary conditions are implicitly handled for arbitrary higher order kinematic models. The validity algorithm is illustrated with examples involving linear elasticity and hyperelasticity. (C) 2013 Elsevier Inc. All rights reserved.