Genetic analysis of an Indian family with members affected with Waardenburg syndrome and Duchenne muscular dystrophy

Purpose: Waardenburg syndrome (WS) is characterized by sensorineural hearing loss and pigmentation defects of the eye, skin, and hair. It is caused by mutations in one of the following genes: PAX3 (paired box 3), MITF (microphthalmia-associated transcription factor), EDNRB (endothelin receptor type B), EDN3 (endothelin 3), SNAI2 (snail homolog 2, Drosophila) and SOX10 (SRY-box containing gene 10). Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutations in the DMD gene. The purpose of this study was to identify the genetic causes of WS and DMD in an Indian family with two patients: one affected with WS and DMD, and another one affected with only WS. Methods: Blood samples were collected from individuals for genomic DNA isolation. To determine the linkage of this family to the eight known WS loci, microsatellite markers were selected from the candidate regions and used to genotype the family. Exon-specific intronic primers for EDN3 were used to amplify and sequence DNA samples from affected individuals to detect mutations. A mutation in DMD was identified by multiplex PCR and multiplex ligation-dependent probe amplification method using exon-specific probes. Results: Pedigree analysis suggested segregation of WS as an autosomal recessive trait in the family. Haplotype analysis suggested linkage of the family to the WS4B (EDN3) locus. DNA sequencing identified a novel missense mutation p.T98M in EDN3. A deletion mutation was identified in DMD. Conclusions: This study reports a novel missense mutation in EDN3 and a deletion mutation in DMD in the same Indian family. The present study will be helpful in genetic diagnosis of this family and increases the mutation spectrum of EDN3.

Functional Analysis of the Genes Encoding Diaminopropionate Ammonia Lyase in Escherichia coli and Salmonella enterica Serovar Typhimurium

Diaminopropionate ammonia lyase (DAPAL) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the conversion of diaminopropionate (DAP) to pyruvate and ammonia and plays an important role in cell metabolism. We have investigated the role of the ygeX gene of Escherichia coli K-12 and its ortholog, STM1002, in Salmonella enterica serovar Typhimurium LT2, presumed to encode DAPAL, in the growth kinetics of the bacteria. While Salmonella Typhimurium LT2 could grow on DL-DAP as a sole carbon source, the wild-type E. coli K-12 strain exhibited only marginal growth on DL-DAP, suggesting that DAPAL is functional in S. Typhimurium. The expression of ygeX in E. coli was low as detected by reverse transcriptase PCR (RT-PCR), consistent with the poor growth of E. coli on DL-DAP. Strains of S. Typhimurium and E. coli with STM1002 and ygeX, respectively, deleted showed loss of growth on DL-DAP, confirming that STM1002 (ygeX) is the locus encoding DAPAL. Interestingly, the presence of DL-DAP caused a growth inhibition of the wild-type E. coli strain as well as the knockout strains of S. Typhimurium and E. coli in minimal glucose/glycerol medium. Inhibition by DL-DAP was rescued by transforming the strains with plasmids containing the STM1002 (ygeX) gene encoding DAPAL or supplementing the medium with Casamino Acids. Growth restoration studies using media lacking specific amino acid supplements suggested that growth inhibition by DL-DAP in the absence of DAPAL is associated with auxotrophy related to the inhibition of the enzymes involved in the biosynthetic pathways of pyruvate and aspartate and the amino acids derived from them.

Analysis of an Interior Penalty Method for Fourth Order Problems on Polygonal Domains

Error analysis for a stable C (0) interior penalty method is derived for general fourth order problems on polygonal domains under minimal regularity assumptions on the exact solution. We prove that this method exhibits quasi-optimal order of convergence in the discrete H (2), H (1) and L (2) norms. L (a) norm error estimates are also discussed. Theoretical results are demonstrated by numerical experiments.

Error exponent analysis of energy-based bayesian spectrum sensing under fading channels

This paper analyzes the error exponents in Bayesian decentralized spectrum sensing, i.e., the detection of occupancy of the primary spectrum by a cognitive radio, with probability of error as the performance metric. At the individual sensors, the error exponents of a Central Limit Theorem (CLT) based detection scheme are analyzed. At the fusion center, a K-out-of-N rule is employed to arrive at the overall decision. It is shown that, in the presence of fading, for a fixed number of sensors, the error exponents with respect to the number of observations at both the individual sensors as well as at the fusion center are zero. This motivates the development of the error exponent with a certain probability as a novel metric that can be used to compare different detection schemes in the presence of fading. The metric is useful, for example, in answering the question of whether to sense for a pilot tone in a narrow band (and suffer Rayleigh fading) or to sense the entire wide-band signal (and suffer log-normal shadowing), in terms of the error exponent performance. The error exponents with a certain probability at both the individual sensors and at the fusion center are derived, with both Rayleigh as well as log-normal shadow fading. Numerical results are used to illustrate and provide a visual feel for the theoretical expressions obtained.

Computationally efficient yet accurate analysis of composite plate

This article does not have an abstract.

Mutation analysis of the SLC4A11 gene in Indian families with congenital hereditary endothelial dystrophy 2 and a review of the literature

Purpose: Congenital hereditary endothelial dystrophy 2 (CHED2) is an autosomal recessive disorder caused by mutations in the solute carrier family 4, sodium borate transporter, member 11 (SLC4A11) gene. The purpose of this study was to identify the genetic cause of CHED2 in six Indian families and catalog all known mutations in the SLC4A11 gene. Methods: Peripheral blood samples were collected from individuals of the families with CHED2 and used in genomic DNA isolation. PCR primers were used to amplify the entire coding region including intron-exon junctions of SLC4A11. Amplicons were subsequently sequenced to identify the mutations. Results: DNA sequence analysis of the six families identified four novel (viz., p.Thr262Ile, p.Gly417Arg, p.Cys611Arg, and p.His724Asp) mutations and one known p.Arg869His homozygous mutation in the SLC4A11 gene. The mutation p.Gly417Arg was identified in two families. Conclusions: This study increases the mutation spectrum of the SLC4A11 gene. A review of the literature showed that the total number of mutations in the SLC4A11 gene described to date is 78. Most of the mutations are missense, followed by insertions-deletions. The present study will be helpful in genetic diagnosis of the families reported here.

Analysis of 20alpha-hydroxysteroid dehydrogenase expression in the corpus luteum of the buffalo cow: effect of prostaglandin F2-alpha treatment on circulating 20alpha-hydroxyprogesterone levels

Background: During female reproductive cycles, a rapid fall in circulating progesterone (P4) levels is one of the earliest events that occur during induced luteolysis in mammals. In rodents, it is well recognized that during luteolysis, P4 is catabolized to its inactive metabolite, 20alpha-hydroxyprogesterone (20alpha-OHP) by the action of 20alpha-hydroxysteroid dehydrogenase (20alpha-HSD) enzyme and involves transcription factor, Nur77. Studies have been carried out to examine expression of 20alpha-HSD and its activity in the corpus luteum (CL) of buffalo cow. Methods: The expression of 20alpha-HSD across different bovine tissues along with CL was examined by qPCR analysis. Circulating P4 levels were monitored before and during PGF2alpha treatment. Expression of 20alpha-HSD and Nur77 mRNA was determined in CL at different time points post PGF2alpha treatment in buffalo cows. The chromatographic separation of P4 and its metabolite, 20alpha-OHP, in rat and buffalo cow serum samples were performed on reverse phase HPLC system. To further support the findings, 20alpha-HSD enzyme activity was quantitated in cytosolic fraction of CL of both rat and buffalo cow. Results: Circulating P4 concentration declined rapidly in response to PGF2alpha treatment. HPLC analysis of serum samples did not reveal changes in circulating 20alpha-OHP levels in buffalo cows but serum from pseudo pregnant rats receiving PGF2alpha treatment showed an increased 20alpha-OHP level at 24 h post treatment with accompanying decrease in P4 concentration. qPCR expression of 20alpha-HSD in CL from control and PGF2alpha-treated buffalo cows showed higher expression at 3 and 18 h post treatment, but its specific activity was not altered at different time points post PGF2alpha treatment. The Nur77 expression increased several fold 3 h post PGF2alpha treatment similar to the increased expression observed in the PGF2alpha-treated pseudo pregnant rats which perhaps suggest initiation of activation of apoptotic pathways in response to PGF2alpha treatment. Conclusions: The results taken together suggest that synthesis of P4 appears to be primarily affected by PGF2alpha treatment in buffalo cows in contrast to increased metabolism of P4 in rodents.

Bivariate frequency analysis of floods using a diffusion based kernel density estimator

Recent focus of flood frequency analysis (FFA) studies has been on development of methods to model joint distributions of variables such as peak flow, volume, and duration that characterize a flood event, as comprehensive knowledge of flood event is often necessary in hydrological applications. Diffusion process based adaptive kernel (D-kernel) is suggested in this paper for this purpose. It is data driven, flexible and unlike most kernel density estimators, always yields a bona fide probability density function. It overcomes shortcomings associated with the use of conventional kernel density estimators in FFA, such as boundary leakage problem and normal reference rule. The potential of the D-kernel is demonstrated by application to synthetic samples of various sizes drawn from known unimodal and bimodal populations, and five typical peak flow records from different parts of the world. It is shown to be effective when compared to conventional Gaussian kernel and the best of seven commonly used copulas (Gumbel-Hougaard, Frank, Clayton, Joe, Normal, Plackett, and Student's T) in estimating joint distribution of peak flow characteristics and extrapolating beyond historical maxima. Selection of optimum number of bins is found to be critical in modeling with D-kernel.

Profiling of Luteal Transcriptome during Prostaglandin F2-Alpha Treatment in Buffalo Cows: Analysis of Signaling Pathways Associated with Luteolysis

In several species including the buffalo cow, prostaglandin (PG) F-2 alpha is the key molecule responsible for regression of corpus luteum (CL). Experiments were carried out to characterize gene expression changes in the CL tissue at various time points after administration of luteolytic dose of PGF(2 alpha) in buffalo cows. Circulating progesterone levels decreased within 1 h of PGF(2 alpha) treatment and evidence of apoptosis was demonstrable at 18 h post treatment. Microarray analysis indicated expression changes in several of immediate early genes and transcription factors within 3 h of treatment. Also, changes in expression of genes associated with cell to cell signaling, cytokine signaling, steroidogenesis, PG synthesis and apoptosis were observed. Analysis of various components of LH/CGR signaling in CL tissues indicated decreased LH/CGR protein expression, pCREB levels and PKA activity post PGF(2 alpha) treatment. The novel finding of this study is the down regulation of CYP19A1 gene expression accompanied by decrease in expression of E-2 receptors and circulating and intra luteal E-2 post PGF(2 alpha) treatment. Mining of microarray data revealed several differentially expressed E-2 responsive genes. Since CYP19A1 gene expression is low in the bovine CL, mining of microarray data of PGF(2 alpha)-treated macaques, the species with high luteal CYP19A1 expression, showed good correlation between differentially expressed E-2 responsive genes between both the species. Taken together, the results of this study suggest that PGF(2 alpha) interferes with luteotrophic signaling, impairs intraluteal E-2 levels and regulates various signaling pathways before the effects on structural luteolysis are manifest.

Virus-sized colloid transport in a single pore: Model development and sensitivity analysis

A mathematical model is developed to simulate the transport and deposition of virus-sized colloids in a cylindrical pore throat considering various processes such as advection, diffusion, colloid-collector surface interactions and hydrodynamic wall effects. The pore space is divided into three different regions, namely, bulk, diffusion and potential regions, based on the dominant processes acting in each of these regions. In the bulk region, colloid transport is governed by advection and diffusion whereas in the diffusion region, colloid mobility due to diffusion is retarded by hydrodynamic wall effects. Colloid-collector interaction forces dominate the transport in the potential region where colloid deposition occurs. The governing equations are non-dimensionalized and solved numerically. A sensitivity analysis indicates that the virus-sized colloid transport and deposition is significantly affected by various pore-scale parameters such as the surface potentials on colloid and collector, ionic strength of the solution, flow velocity, pore size and colloid size. The adsorbed concentration and hence, the favorability of the surface for adsorption increases with: (i) decreasing magnitude and ratio of surface potentials on colloid and collector, (ii) increasing ionic strength and (iii) increasing pore radius. The adsorbed concentration increases with increasing Pe, reaching a maximum value at Pe = 0.1 and then decreases thereafter. Also, the colloid size significantly affects particle deposition with the adsorbed concentration increasing with increasing particle radius, reaching a maximum value at a particle radius of 100 nm and then decreasing with increasing radius. System hydrodynamics is found to have a greater effect on larger particles than on smaller ones. The secondary minimum contribution to particle deposition has been found to increase as the favorability of the surface for adsorption decreases. The sensitivity of the model to a given parameter will be high if the conditions are favorable for adsorption. The results agree qualitatively with the column-scale experimental observations available in the literature. The current model forms the building block in upscaling colloid transport from pore scale to Darcy scale using Pore-Network Modeling. (C) 2014 Elsevier By. All rights reserved.

Nonlinear analysis of a thin pre-twisted and delaminated anisotropic strip

The present work is aimed at the development of an efficient mathematical model to assess the degradation in the stiffness properties of an anisotropic strip due to delamination. In particular, the motive is to capture those nonlinear effects in a strip that arise due to the geometry of the structure, in the presence of delamination. The variational asymptotic method (VAM) is used as a mathematical tool to simplify the original 3D problem to a 1D problem. Further simplification is achieved by modeling the delaminated structure by a sublaminate approach. By VAM, a 2D nonlinear sectional analysis is carried out to determine compact expression for the stiffness terms. The stiffness terms, both linear and nonlinear, are derived as functions of delamination length and location in closed form. In general, the results from the analysis include fully coupled nonlinear 1D stiffness coefficients, 3D strain field, 3D stress field, and in-plane and warping fields. In this work, the utility of the model is demonstrated for a static case, and its capability to capture the trapeze effect in the presence of delamination is investigated and compared with results available in the literature.

Flow Cytometry Analysis of Cytotoxicity In Vitro and Long-Term Toxicity of HA-40wt% BaTiO3 Nanoparticles In Vivo

The development of new implantable biomaterials requires bone-mimicking physical properties together with desired biocompatible property. In continuation to our earlier published research to establish compositional dependent multifunctional bone-like properties and cytocompatibility response of hydroxyapatite (HA)-BaTiO3 composites, the toxicological property evaluation, both invitro and invivo, were conducted on HA-40wt% BaTiO3 and reported in this work. In particular, this work reports invitro cytotoxicity of mouse myoblast cells as well as invivo long-term tissue and nanoparticles interaction of intra-articularly injected HA-40wt% BaTiO3 and BaTiO3 up to the concentration of 25mg/mL in physiological saline over 12weeks in mouse model. The careful analysis of flow cytometry results could not reveal any statistically significant difference in terms of early/late apoptotic cells or necrotic cells over 8d in culture. Extensive histological analysis could not record any signature of cellular level toxicity or pronounced inflammatory response in vital organs as well as at knee joints of Balb/c mice after 12weeks. Taken together, this study establishes nontoxic nature of HA-40wt% BaTiO3 and therefore, HA-40wt% BaTiO3 can be used safely for various biomedical applications.

Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase

Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.

Global response sensitivity analysis of uncertain structures

The problem of characterizing global sensitivity indices of structural response when system uncertainties are represented using probabilistic and (or) non-probabilistic modeling frameworks (which include intervals, convex functions, and fuzzy variables) is considered. These indices are characterized in terms of distance measures between a fiducial model in which uncertainties in all the pertinent variables are taken into account and a family of hypothetical models in which uncertainty in one or more selected variables are suppressed. The distance measures considered include various probability distance measures (Hellinger,l(2), and the Kantorovich metrics, and the Kullback-Leibler divergence) and Hausdorff distance measure as applied to intervals and fuzzy variables. Illustrations include studies on an uncertainly parametered building frame carrying uncertain loads. (C) 2015 Elsevier Ltd. All rights reserved.

Efficient coupled polynomial interpolation scheme for out-of-plane free vibration analysis of curved beams

The performance of two curved beam finite element models based on coupled polynomial displacement fields is investigated for out-of-plane vibration of arches. These two-noded beam models employ curvilinear strain definitions and have three degrees of freedom per node namely, out-of-plane translation (v), out-of-plane bending rotation (theta(z)) and torsion rotation (theta(s)). The coupled polynomial interpolation fields are derived independently for Timoshenko and Euler-Bernoulli beam elements using the force-moment equilibrium equations. Numerical performance of these elements for constrained and unconstrained arches is compared with the conventional curved beam models which are based on independent polynomial fields. The formulation is shown to be free from any spurious constraints in the limit of `flexureless torsion' and `torsionless flexure' and hence devoid of flexure and torsion locking. The resulting stiffness and consistent mass matrices generated from the coupled displacement models show excellent convergence of natural frequencies in locking regimes. The accuracy of the shear flexibility added to the elements is also demonstrated. The coupled polynomial models are shown to perform consistently over a wide range of flexure-to-shear (EI/GA) and flexure-to-torsion (EI/GJ) stiffness ratios and are inherently devoid of flexure, torsion and shear locking phenomena. (C) 2015 Elsevier B.V. All rights reserved.