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.

Support vector machine for evaluating seismic-liquefaction potential using shear wave velocity

The use of the shear wave velocity data as a field index for evaluating the liquefaction potential of sands is receiving increased attention because both shear wave velocity and liquefaction resistance are similarly influenced by many of the same factors such as void ratio, state of stress, stress history and geologic age. In this paper, the potential of support vector machine (SVM) based classification approach has been used to assess the liquefaction potential from actual shear wave velocity data. In this approach, an approximate implementation of a structural risk minimization (SRM) induction principle is done, which aims at minimizing a bound on the generalization error of a model rather than minimizing only the mean square error over the data set. Here SVM has been used as a classification tool to predict liquefaction potential of a soil based on shear wave velocity. The dataset consists the information of soil characteristics such as effective vertical stress (sigma'(v0)), soil type, shear wave velocity (V-s) and earthquake parameters such as peak horizontal acceleration (a(max)) and earthquake magnitude (M). Out of the available 186 datasets, 130 are considered for training and remaining 56 are used for testing the model. The study indicated that SVM can successfully model the complex relationship between seismic parameters, soil parameters and the liquefaction potential. In the model based on soil characteristics, the input parameters used are sigma'(v0), soil type. V-s, a(max) and M. In the other model based on shear wave velocity alone uses V-s, a(max) and M as input parameters. In this paper, it has been demonstrated that Vs alone can be used to predict the liquefaction potential of a soil using a support vector machine model. (C) 2010 Elsevier B.V. All rights reserved.

Ultrafast underdamped solvation: Agreement between computer simulation and various theories of solvation dynamics

A theoretical analysis of the three currently popular microscopic theories of solvation dynamics, namely, the dynamic mean spherical approximation (DMSA), the molecular hydrodynamic theory (MHT), and the memory function theory (MFT) is carried out. It is shown that in the underdamped limit of momentum relaxation, all three theories lead to nearly identical results when the translational motions of both the solute ion and the solvent molecules are neglected. In this limit, the theoretical prediction is in almost perfect agreement with the computer simulation results of solvation dynamics in the model Stockmayer liquid. However, the situation changes significantly in the presence of the translational motion of the solvent molecules. In this case, DMSA breaks down but the other two theories correctly predict the acceleration of solvation in agreement with the simulation results. We find that the translational motion of a light solute ion can play an important role in its own solvation. None of the existing theories describe this aspect. A generalization of the extended hydrodynamic theory is presented which, for the first time, includes the contribution of solute motion towards its own solvation dynamics. The extended theory gives excellent agreement with the simulations where solute motion is allowed. It is further shown that in the absence of translation, the memory function theory of Fried and Mukamel can be recovered from the hydrodynamic equations if the wave vector dependent dissipative kernel in the hydrodynamic description is replaced by its long wavelength value. We suggest a convenient memory kernel which is superior to the limiting forms used in earlier descriptions. We also present an alternate, quite general, statistical mechanical expression for the time dependent solvation energy of an ion. This expression has remarkable similarity with that for the translational dielectric friction on a moving ion.

Expression of microinjected foreign DNA in silkworm,bombyx mori

As a prelude to achieving transgenesis in Bombyx mori, conditions have been established for successful microinjection of cloned foreign genes into the silk worm eggs. A sharpened metallic needle is used to pierce the thick chorion layer of the eggsheil, approaching through a droplet of DNA solution deposited on its surface. The microinjection is carried out within 2-2.5 h after oviposition and the injected eggs show 3-5% hatchability and 80-90% survival. Such larvae continuously expressed the microinjected cloned reporter gene, beta-galactosidase, placed under the control of a constitutively expressed cytoplasmic actin A3 gene promoter from B. mori. The expression is seen in different tissues, viz. the fat body, tracheae and the silk glands, till the late larval instars. The microinjected DNA sequences are retained in the adult G(o) moths.

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.

Receiver-Only Optimized Vector Quantization for Noisy Channels

This paper considers the design and analysis of a filter at the receiver of a source coding system to mitigate the excess Mean-Squared Error (MSE) distortion caused due to channel errors. It is assumed that the source encoder is channel-agnostic, i.e., that a Vector Quantization (VQ) based compression designed for a noiseless channel is employed. The index output by the source encoder is sent over a noisy memoryless discrete symmetric channel, and the possibly incorrect received index is decoded by the corresponding VQ decoder. The output of the VQ decoder is processed by a receive filter to obtain an estimate of the source instantiation. In the sequel, the optimum linear receive filter structure to minimize the overall MSE is derived, and shown to have a minimum-mean squared error receiver type structure. Further, expressions are derived for the resulting high-rate MSE performance. The performance is compared with the MSE obtained using conventional VQ as well as the channel optimized VQ. The accuracy of the expressions is demonstrated through Monte Carlo simulations.

Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein

The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished, A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.

A vector measure for the intelligence of a question-answering (Q-A) system

The problem of quantification of intelligence of humans, and of intelligent systems, has been a challenging and controversial topic. IQ tests have been traditionally used to quantify human intelligence based on results of test designed by psychologists. It is in general very difficult to quantify intelligence. In this paper the authors consider a simple question-answering (Q-A) system and use this to quantify intelligence. The authors quantify intelligence as a vector with three components. The components consist of a measure of knowledge in asking questions, effectiveness of questions asked, and correctness of deduction. The authors formalize these parameters and have conducted experiments on humans to measure these parameters

Baculovirus mediated high-level expression of luciferase in silkworm cells and larvae

Bombyx mori nuclear polyhedrosis virus (BmNPV)-based baculovirus expression system exploits silkworm larvae as an economical alternative to large-scale cell cultures for production of biomolecules. To generate recombinant BmNPV at high efficiency, we have achieved high efficiency transfection of B. mori cells, BmN, through lipofection. Optimal conditions for lipofection were standardized by quantification of the transient expression level of firefly luciferase (luc) reporter gene under control of an immediate early gene promoter of BmNPV Lipofection was 50-fold and 100-fold more efficient than the calcium phosphate method for transfecting BmN and Sf9 cells, respectively. Lipofection enabled us to generate a recombinant BmNPV (vBmluc), harboring luc under control of the strong polyhedrin promoter On infection with vBmluc, luciferase was expressed at very high levels, 170 mu g/10(6) BmN cells or 13 mg/larva. Expression of luciferase in vBmluc-infected larvae was visualized by luminescence emission instantaneously following luciferin injection generating ''glowing silkworms''.

KFVS (Kinetic Flux Vector Splitting) on moving grids for unsteady aerodynamics

Accurate numerical solutions to the problems in fluid-structure (aeroelasticity) interaction are becoming increasingly important in recent years. The methods based on FCD (Fixed Computational Domain) and ALE (Alternate Lagrangian Eulerian) to solve such problems suffer from numerical instability and loss of accuracy. They are not general and can not be extended to the flowsolvers on unstructured meshes. Also, global upwind schemes can not be used in ALE formulation thus leads to the development of flow solvers on moving grids. The KFVS method has been shown to be easily amenable on moving grids required in unsteady aerodynamics. The ability of KFMG (Kinetic Flux vector splitting on Moving Grid) Euler solver in capturing shocks, expansion waves with small and very large pressure ratios and contact discontinuities has been demonstrated.

A Ten-microRNA Expression Signature Predicts Survival in Glioblastoma

Glioblastoma (GBM) is the most common and aggressive primary brain tumor with very poor patient median survival. To identify a microRNA (miRNA) expression signature that can predict GBM patient survival, we analyzed the miRNA expression data of GBM patients (n = 222) derived from The Cancer Genome Atlas (TCGA) dataset. We divided the patients randomly into training and testing sets with equal number in each group. We identified 10 significant miRNAs using Cox regression analysis on the training set and formulated a risk score based on the expression signature of these miRNAs that segregated the patients into high and low risk groups with significantly different survival times (hazard ratio HR] = 2.4; 95% CI = 1.4-3.8; p < 0.0001). Of these 10 miRNAs, 7 were found to be risky miRNAs and 3 were found to be protective. This signature was independently validated in the testing set (HR = 1.7; 95% CI = 1.1-2.8; p = 0.002). GBM patients with high risk scores had overall poor survival compared to the patients with low risk scores. Overall survival among the entire patient set was 35.0% at 2 years, 21.5% at 3 years, 18.5% at 4 years and 11.8% at 5 years in the low risk group, versus 11.0%, 5.5%, 0.0 and 0.0% respectively in the high risk group (HR = 2.0; 95% CI = 1.4-2.8; p < 0.0001). Cox multivariate analysis with patient age as a covariate on the entire patient set identified risk score based on the 10 miRNA expression signature to be an independent predictor of patient survival (HR = 1.120; 95% CI = 1.04-1.20; p = 0.003). Thus we have identified a miRNA expression signature that can predict GBM patient survival. These findings may have implications in the understanding of gliomagenesis, development of targeted therapy and selection of high risk cancer patients for adjuvant therapy.

Expression of the Japanese encephalitis virus NS3 and NS2b proteins as glutathione S-transferase fusions

Flaviviruses generate their structural and nonstructural proteins by proteolytic processing of a single large polyprotein precursor. These proteolytic events are brought about both by host cell signalase and a virally encoded protease. The virally encoded proteolytic activity has been shown to reside within the nonstructural protein 3 (NS3) and requires the product of the nonstructural 2b (NS2b) gene. In order to obtain sufficient quantities of pure NS2b and NS3 proteins for kinetic analysis, we have expressed both these proteins in recombinant systems as fusions to glutathione S-transferase (GST). The fusion constructs were driven by the strong bacteriophage T7 promoter. Transfection of these constructs into the African green monkey kidney cell line CV-1 previously infected with a recombinant vaccinia virus expressing the T7 RNA polymerase resulted in synthesis of the fusion proteins. Both the fusion proteins could be purified to homogeneity in a single step using a glutathione agarose affinity matrix.