A monolithic strategy for fluid-structure interaction problems

In this work, we present a new monolithic strategy for solving fluid-structure interaction problems involving incompressible fluids, within the context of the finite element method. This strategy, similar to the continuum dynamics, conserves certain properties, and thus provides a rational basis for the design of the time-stepping strategy; detailed proofs of the conservation of these properties are provided. The proposed algorithm works with displacement and velocity variables for the structure and fluid, respectively, and introduces no new variables to enforce velocity or traction continuity. Any existing structural dynamics algorithm can be used without change in the proposed method. Use of the exact tangent stiffness matrix ensures that the algorithm converges quadratically within each time step. An analytical solution is presented for one of the benchmark problems used in the literature, namely, the piston problem. A number of benchmark problems including problems involving free surfaces such as sloshing and the breaking dam problem are used to demonstrate the good performance of the proposed method. Copyright (C) 2010 John Wiley & Sons, Ltd.

Specificity in the regulation of eukaryotic gene transcription

The regulation of eukaryotic gene transcription poses major challenges in terms of the innumerable protein factors required to ensure tissue or cell-type specificity. While this specificity is sought to be explained by the interaction of cis-acting DNA elements and thetrans-acting protein factor(s), considerable amount of degeneracy has been observed in this interaction. Immunoglobulin heavy chain gene expression in B cells and liver-specific gene expression are discussed as examples of this complexity in this article. Heterodimerization and post-translational modification of transcription factors and the organization of composite promoter elements are strategies by which diverse sets of genes can be regulated in a specific manner using a finite number of protein factors

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

The effect of progesterone replacement on gene expression in the corpus luteum during induced regression and late luteal phase in the bonnet monkey (Macaca radiata)

Background: In higher primates, although LH/CG play a critical role in the control of corpus luteum (CL) function, the direct effects of progesterone (P4) in the maintenance of CL structure and function are unclear. Several experiments were conducted in the bonnet monkey to examine direct effects of P4 on gene expression changes in the CL, during induced luteolysis and the late luteal phase of natural cycles. Methods: To identify differentially expressed genes encoding PR, PR binding factors, cofactors and PR downstream signaling target genes, the genome-wide analysis data generated in CL of monkeys after LH/P-4 depletion and LH replacement were mined and validated by real-time RT-PCR analysis. Initially, expression of these P4 related genes were determined in CL during different stages of luteal phase. The recently reported model system of induced luteolysis, yet capable of responsive to tropic support, afforded an ideal situation to examine direct effects of P4 on structure and function of CL. For this purpose, P4 was infused via ALZET pumps into monkeys 24 h after LH/P4 depletion to maintain mid luteal phase circulating P4 concentration (P4 replacement). In another experiment, exogenous P4 was supplemented during late luteal phase to mimic early pregnancy. Results: Based on the published microarray data, 45 genes were identified to be commonly regulated by LH and P4. From these 19 genes belonging to PR signaling were selected to determine their expression in LH/P-4 depletion and P4 replacement experiments. These 19 genes when analyzed revealed 8 genes to be directly responsive to P4, whereas the other genes to be regulated by both LH and P4. Progesterone supplementation for 24 h during the late luteal phase also showed changes in expression of 17 out of 19 genes examined. Conclusion: These results taken together suggest that P4 regulates, directly or indirectly, expression of a number of genes involved in the CL structure and function.

Salmonella enterica Serovar Typhimurium Lacking hfq Gene Confers Protective Immunity against Murine Typhoid

Salmonella enterica is an important enteric pathogen and its various serovars are involved in causing both systemic and intestinal diseases in humans and domestic animals. The emergence of multidrug-resistant strains of Salmonella leading to increased morbidity and mortality has further complicated its management. Live attenuated vaccines have been proven superior over killed or subunit vaccines due to their ability to induce protective immunity. Of the various strategies used for the generation of live attenuated vaccine strains, focus has gradually shifted towards manipulation of virulence regulator genes. Hfq is a RNA chaperon which mediates the binding of small RNAs to the mRNA and assists in post-transcriptional gene regulation in bacteria. In this study, we evaluated the efficacy of the Salmonella Typhimurium Dhfq strain as a candidate for live oral vaccine in murine model of typhoid fever. Salmonella hfq deletion mutant is highly attenuated in cell culture and animal model implying a significant role of Hfq in bacterial virulence. Oral immunization with the Salmonella hfq deletion mutant efficiently protects mice against subsequent oral challenge with virulent strain of Salmonella Typhimurium. Moreover, protection was induced upon both multiple as well as single dose of immunizations. The vaccine strain appears to be safe for use in pregnant mice and the protection is mediated by the increase in the number of CD4(+) T lymphocytes upon vaccination. The levels of serum IgG and secretory-IgA in intestinal washes specific to lipopolysaccharide and outer membrane protein were significantly increased upon vaccination. Furthermore, hfq deletion mutant showed enhanced antigen presentation by dendritic cells compared to the wild type strain. Taken together, the studies in murine immunization model suggest that the Salmonella hfq deletion mutant can be a novel live oral vaccine candidate.

Theoretical and experimental investigation of framed structure-layered soil interaction problems

The plane stress solution for the interaction analysis of a framed structure, with a foundation beam, resting on a layered soil has been studied using both theoretical and photoelastic methods. The theoretical analysis has been done by using a combined analytical and finite element method. In this, the analytical solution has been used for the semi-infinite layered medium and finite element method for the framed structure. The experimental investigation has been carried out using two-dimensional photoelasticity in which modelling of the layered semi-infinite plane and a method to obtain contact pressure distribution have been discussed. The theoretical and experimental results in respect of contact pressure distribution between the foundation beam and layered soil medium, the fibre stresses in the foundation beam and framed structure have been compared. These results have also been compared with theoretical results obtained by idealizing the layered semi-infinite plane as (a) a Winkler model and (b) an equivalent homogeneous semi-infinite medium

A general procedure for modified crack closure integral in 3D problems with cracks

In linear elastic fracture mechanics (LEFM), Irwin's crack closure integral (CCI) is one of the signficant concepts for the estimation of strain energy release rates (SERR) G, in individual as well as mixed-mode configurations. For effective utilization of this concept in conjunction with the finite element method (FEM), Rybicki and Kanninen [Engng Fracture Mech. 9, 931 938 (1977)] have proposed simple and direct estimations of the CCI in terms of nodal forces and displacements in the elements forming the crack tip from a single finite element analysis instead of the conventional two configuration analyses. These modified CCI (MCCI) expressions are basically element dependent. A systematic derivation of these expressions using element stress and displacement distributions is required. In the present work, a general procedure is given for the derivation of MCCI expressions in 3D problems with cracks. Further, a concept of sub-area integration is proposed which facilitates evaluation of SERR at a large number of points along the crack front without refining the finite element mesh. Numerical data are presented for two standard problems, a thick centre-cracked tension specimen and a semi-elliptical surface crack in a thick slab. Estimates for the stress intensity factor based on MCCI expressions corresponding to eight-noded brick elements are obtained and compared with available results in the literature.

Post-transcriptional Repair of a Split Heat Shock Protein 90 Gene by mRNA trans-Splicing

Heat shock protein 90 participates in diverse biological processes ranging from protein folding, cell cycle, signal transduction and development to evolution in all eukaryotes. It is also critically involved in regulating growth of protozoa such as Dictyostelium discoideum, Leishmania donovani, Plasmodium falciparum, Trypanosoma cruzi, and Trypanosoma evansi. Selective inhibition of Hsp90 has also been explored as an intervention strategy against important human diseases such as cancer, malaria, or trypanosomiasis. Giardia lamblia, a simple protozoan parasite of humans and animals, is an important cause of diarrheal disease with significant morbidity and some mortality in tropical countries. Here we show that the G. lamblia cytosolic hsp90 ( glhsp90) is split in two similar sized fragments located 777 kb apart on the same scaffold. Intrigued by this unique arrangement, which appears to be specific for the Giardiinae, we have investigated the biosynthesis of GlHsp90. We used genome sequencing to confirm the split nature of the giardial hsp90. However, a specific antibody raised against the peptide detected a product with a mass of about 80 kDa, suggesting a post-transcriptional rescue of the genomic defect. We show evidence for the joining of the two independent Hsp90 transcripts in-trans to one long mature mRNA presumably by RNA splicing. The splicing junction carries hallmarks of classical cis-spliced introns, suggesting that the regular cis-splicing machinery may be sufficient for repair of the open reading frame. A complementary 26-nt sequence in the ``intron'' regions adjacent to the splice sites may assist in positioning the two pre-mRNAs for processing. This is the first example of post-transcriptional rescue of a split gene by trans-splicing.

Dendritic Poly(ether imine) Based Gene Delivery Vector

The nonviral vector based gene delivery approach is attractive due to advantages associated with molecular-level modifications suitable for optimization of vector properties. In a new class of nonviral gene delivery systems, we herein report the potential of poly(ether Mine) (PETIM) dendrimers to mediate an effective gene delivery function. PETIM dendrimer, constituted with tertiary amine branch points, n-propyl ether linkers and primary amines at their peripheries, exhibits significantly reduced toxicities, over a broad concentration range. The dendrimer complexes pDNA effectively, protects DNA from endosomal damages, and delivers to the cell nucleus. Gene transfection studies, utilizing a reporter plasmid pEGFP-C1 and upon complexation with dendrimer, showed a robust expression of the encoded protein. The study shows that PETIM dendrimers are hitherto unknown novel gene delivery vectors, combining features of poly(ethylene imine)-based polymers and dendrimers, yet are relatively nontoxic and structurally precise.

Modified Crack Closure Integral (MCCI) For 3-D Problems Using 20-Noded Brick Elements

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

Contraceptive vaccines: current status and problems in mass application

Progress in the development of contraceptive vaccines for males and females is reviewed. Based on the criteria which need to be met with, none of the proposed candidate antigens meets the requirements for use as a contraceptive vaccine for human application. One of the major problems is the need for periodic injections to maintain required titre and use of an alternate method until effective titres are obtained. Some of the problems associated with active immunization approach can be overcome by the use of preformed, highly specific, potent antibodies. Some progress has been achieved in this direction by the use of humanized single chain monoclonal antibodies to human chorionic gonadotropin.

Modified crack closure integral (MCCI) for 3-d problems using 20 noded brick elememnts

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

Cardiac remodeling in Drosophila arises from changes in actin gene expression and from a contribution of lymph gland-like cells to the heart musculature

Understanding the basis of normal heart remodeling can provide insight into the plasticity of the cardiac state, and into the potential for treating diseased tissue. In Drosophila, the adult heart arises during metamorphosis from a series of events, that include the remodeling of an existing cardiac tube, the elaboration of new inflow tracts, and the addition of a layer of longitudinal muscle fibers. We have identified genes active in all these three processes, and studied their expression in order to characterize in greater detail normal cardiac remodeling. Using a Transglutaminase-lacZ transgenic line, that is expressed in the inflow tracts of the larval and adult heart, we confirm the existence of five inflow tracts in the adult structure. In addition, expression of the Actin87E actin gene is initiated in the remodeling cardiac tube, but not in the longitudinal fibers, and we have identified an Act87E promoter fragment that recapitulates this switch in expression. We also establish that the longitudinal fibers are multinucleated, characterizing these cells as specialized skeletal muscles. Furthermore, we have defined the origin of the longitudinal fibers, as a subset of lymph gland cells associated with the larval dorsal vessel. These studies underline the myriad contributors to the formation of the adult Drosophila heart, and provide new molecular insights into the development of this complex organ. (C) 2011 Elsevier Ireland Ltd. All rights reserved.