Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

A Comparative Study of the Effect of Metallic Au and ReO3 Nanoparticles on the Performance of Silicon Solar Cells

The influence of gold (similar to 35 nm diameter) as well as ReO3 (similar to 17 nm diameter) nanoparticles placed atop silicon photovoltaic devices on absorption and photocurrent generation has been investigated. The nanoparticles improve the power transmission into the semiconductor and consequently, the photocurrent response at wavelengths corresponding to plasmon absorption. An increase in short circuit current up to 4.5% under simulated solar irradiation was observed with the ReO3 nanoparticles, while the gold nanoparticles showed enhancements up to 6.5%. The increase in photocurrent is observed at wavelengths corresponding to the maxima in the surface plasmon resonance absorption spectra. (C) 2010 The Japan Society of Applied Physics

Comparative study of different formulations and solution methods for two phase flow in saturated porous media

Six models (Simulators) are formulated and developed with all possible combinations of pressure and saturation of the phases as primary variables. A comparative study between six simulators with two numerical methods, conventional simultaneous and modified sequential methods are carried out. The results of the numerical models are compared with the laboratory experimental results to study the accuracy of the model especially in heterogeneous porous media. From the study it is observed that the simulator using pressure and saturation of the wetting fluid (PW, SW formulation) is the best among the models tested. Many simulators with nonwetting phase as one of the primary variables did not converge when used along with simultaneous method. Based on simulator 1 (PW, SW formulation), a comparison of different solution methods such as simultaneous method, modified sequential and adaptive solution modified sequential method are carried out on 4 test problems including heterogeneous and randomly heterogeneous problems. It is found that the modified sequential and adaptive solution modified sequential methods could save the memory by half and as also the CPU time required by these methods is very less when compared with that using simultaneous method. It is also found that the simulator with PNW and PW as the primary variable which had problem of convergence using the simultaneous method, converged using both the modified sequential method and also using adaptive solution modified sequential method. The present study indicates that pressure and saturation formulation along with adaptive solution modified sequential method is the best among the different simulators and methods tested.

X-ray studies on crystalline complexes involving amino acids and peptides. XXV. Structures of DL-proline hemisuccinic acid and glycyl-L-histidinium semisuccinate monohydrate and a comparative study of amino-acid and peptide complexes of succinic acid

DL-Proline hemisuccinic acid, C5H9NO2.1/2C4H6O4, M(r) = 174.2, P2(1/c) a = 5.254 (1), b = 17.480 (1), c = 10.230 (i) angstrom, beta = 119.60 (6)-degrees Z = 4, D(m) = 1.41 (4), D(x) = 1.42 g cm-3, R = 0.045 for 973 observed reflections. Glycyl-L-histidinium semisuccinate monohydrate, C8H13N4O3+.C4H5O4-.H2O, M(r) = 348.4, P2(1), a = 4.864 (1), b = 17.071 (2), c = 9.397 (1) angstrom, beta = 90.58-degrees, Z = 2, D(m) = 1.45 (1), D(x) = 1.48 g cm-3, R = 0.027 for 1610 observed reflections. Normal amino-acid and dipeptide aggregation patterns are preserved in the structures in spite of the presence of succinic acid/semisuccinate ions. In both the structures, the amino-acid/dipeptide layers stack in such a way that the succinic acid molecules/semisuccinate ions are enclosed in voids created during stacking. Substantial variability in the ionization state and the stoichiometry is observed in amino-acid and peptide complexes of succinic acid. Succinic acid molecules and succinate ions appear to prefer a planar centro-symmetric conformation with the two carboxyl (carboxylate) groups trans with respect to the central C=C bond. Considerable variation is seen in the departure from and modification of normal amino-acid aggregation patterns produced by the presence of succinic acid. Some of the complexes can be described as inclusion compounds with the amino acid/dipeptide as the 'host' and succinic acid/semisuccinate/succinate as the 'guest'. The effects of change in chirality, though very substantial, are not the same in different pairs of complexes involving DL and L isomers of the same amino acid.

A comparative study of the interaction of nickel clusters with buckminsterfullerene, C60, and graphite

Interaction of nickel deposited on multilayer films of C60 has been investigated in comparison with that on amorphized graphite by employing photoemission spectroscopy. It is shown that unlike with graphite, Ni interacts strongly with C60 causing large changes in C(1s) and C(2p) binding energies. The increase in the Ni(2p) binding energy at small Ni coverages is also far greater on c60 than on graphite.

Prediction of load-deflection behaviour using fracture energy GF: A comparative study of two fracture models for concrete

Load-deflection curves for a notched beam under three-point load are determined using the Fictitious Crack Model (FCM) and Blunt Crack Model (BCM). Two values of fracture energy GF are used in this analysis: (i) GF obtained from the size effect law and (ii) GF obtained independently of the size effect. The predicted load-deflection diagrams are compared with the experimental ones obtained for the beams tested by Jenq and Shah. In addition, the values of maximum load (Pmax) obtained by the analyses are compared with the experimental ones for beams tested by Jenq and Shah and by Bažant and Pfeiffer. The results indicate that the descending portion of the load-deflection curve is very sensitive to the GF value used.

A comparative-study of vapor-compression refrigeration working fluids, in the wake of the montreal protocal

A comparative study has been carried out of R-12, 22, 125, 134a, 152a, 218, 245, 500, 502, 507 and 717 as working fluids in a vapour-compression refrigeration system. Two performance parameters were defined, which are expressed in reduced quantities for a corresponding-states comparison of these refrigerants in the temperature range -20 to 50-degrees-C. One is based on the product of temperature drop to pressure penalty ratio and the available volumetric heat of vaporisation at the evaporator; the other considers the effect of isentropic compression in the ideal gas state. It was shown that R-125, 507 and 218 could be better alternatives to R-12 than R-134a. Among these, R-218 has a lower maximum cycle pressure.

A survey of indian logic from the point of view of computer science

Indian logic has a long history. It somewhat covers the domains of two of the six schools (darsanas) of Indian philosophy, namely, Nyaya and Vaisesika. The generally accepted definition of Indian logic over the ages is the science which ascertains valid knowledge either by means of six senses or by means of the five members of the syllogism. In other words, perception and inference constitute the subject matter of logic. The science of logic evolved in India through three ages: the ancient, the medieval and the modern, spanning almost thirty centuries. Advances in Computer Science, in particular, in Artificial Intelligence have got researchers in these areas interested in the basic problems of language, logic and cognition in the past three decades. In the 1980s, Artificial Intelligence has evolved into knowledge-based and intelligent system design, and the knowledge base and inference engine have become standard subsystems of an intelligent system. One of the important issues in the design of such systems is knowledge acquisition from humans who are experts in a branch of learning (such as medicine or law) and transferring that knowledge to a computing system. The second important issue in such systems is the validation of the knowledge base of the system i.e. ensuring that the knowledge is complete and consistent. It is in this context that comparative study of Indian logic with recent theories of logic, language and knowledge engineering will help the computer scientist understand the deeper implications of the terms and concepts he is currently using and attempting to develop.

A comparative study of the interaction of CO with Cu and Cu-Zn alloy clusters

Interaction of CO with Cu clusters deposited on a ZnO(0001) crystal and on ZnO/Zn surfaces (prepared in the electron spectrometer) has been examined by UV and X-ray photoelectron spectroscopy. The interaction is stronger with the small Cu clusters deposited on ZnO/Zn surfaces. Interaction of CO is evert stronger with annealed Cu/ZnO/Zn surfaces where Cu-Zn alloy particles are present. Copyright (C) 1996 Published by Elsevier Science Ltd

A Comparative Study of Electrical Switching Behavior of Certain Tellurium based Chalcogenide Thin Films for Phase Change Memory (PCM) Applications

This work describes the electrical switching behavior of three telluride based amorphous chalcogenide thin film samples, Al-Te, Ge-Se-Te and Ge-Te-Si. These amorphous thin films are made using bulk glassy ingots, prepared by conventional melt quenching technique, using flash evaporation technique; while Al-Te sample has been coated in coplanar electrode geometry, Ge-Se-Te and Ge-Te-Si samples have been deposited with sandwich electrodes. It is observed that all the three samples studied, exhibit memory switching behavior in thin film form, with Ge-Te-Si sample exhibiting a faster switching characteristic. The difference seen in the switching voltages of the three samples studied has been understood on the basis of difference in device geometry and thickness. Scanning electron microscopic image of switched region of a representative Ge15Te81Si4 sample shows a structural change and formation of crystallites in the electrode region, which is responsible for making a conducting channel between the two electrodes during switching.

Comparative Nucleotide and Amino Acid Sequence Analysis of the Sequence-Specific RNA-Binding Rotavirus Nonstructural Protein NSP3

NSP3, an acidic nonstructural protein, encoded by gene 7 has been implicated as the key player in the assembly of the 11 viral plus-strand RNAs into the early replication intermediates during rotavirus morphogenesis. To date, the sequence or NSP3 from only three animal rotaviruses (SA11, SA114F, and bovine UK) has been determined and that from a human strain has not been reported. To determine the genetic diversity among gene 7 alleles from group A rotaviruses, the nucleotide sequence of the NSP3 gene from 13 strains belonging to nine different G serotypes, from both humans and animals, has been determined. Based on the amino acid sequence identity as well as phylogenetic analysis, NSP3 from group A rotaviruses falls into three evolutionarily related groups, i.e., the SA11 group, the Wa group, and the S2 group. The SA 11/SA114F gene appears to have a distant ancestral origin from that of the others and codes for a polypeptide of 315 amino acids (aa) in length. NSP3 from all other group A rotaviruses is only 313 aa in length because of a 2-amino-acid deletion near the carboxy-terminus, While the SA114F gene has the longest 3' untranslated region (UTR) of 132 nucleotides, that from other strains suffered deletions of varying lengths at two positions downstream of the translational termination codon. In spite of the divergence of the nucleotide (nt) sequence in the protein coding region, a stretch of about 80 nt in the 3' UTR is highly conserved in the NSP3 gene from all the strains. This conserved sequence in the 3' UTR might play an important role in the regulation of expression of the NSP3 gene. (C) 1995 Academic Press, Inc.

Comparative studies on the effects of specific immunoneutralization of endogenous FSH or LH on testicular germ cell transformations in the adult bonnet monkey (Macaca radiata)

PROBLEM: It is yet to be determined clearly whether the two hormones FSH and T act synergistically in the same cell type-the Sertoli cells-to control overall spermatogenesis or influence independently the transformation of specific germ cell types during spermatogenesis in the adult mammal. METHOD: Adult male bonnet monkeys specifically deprived of either FSH or LH using immunoneutralization techniques were monitored for changes in testicular germ cell transformation by DNA flow cytometry. RESULTS: FSH deprivation caused a significant reduction (>40%; P < 0.05) in [H-3] thymidine incorporation into DNA of proliferating 2C (spermatogonial) cells, a marked inhibition (>50%) in the transformation of 2C to primary spermatocytes (4C) and a concomitant, belated reduction (50%) in the formation of round spermatids (1C). In contrast, specific LH/T deprivation led to an immediate arrest in the meiotic transformation of 4C to 1C/HC leading to an effective and significant block (<90%; P < 0.01) in sperm production. CONCLUSION: Thus, LH rather than FSH deprivation has a more pronounced and immediate effect as the former primarily blocks meiosis (4C --> 1C/HC) which controls production of spermatids. These data provide evidence for LH/T and FSH regulating spermatogenic process in the adult primate by primarily acting at specific germ cell transformation steps.