Interplay between multiple length and time scales in complex chemical systems

Processes in complex chemical systems, such as macromolecules, electrolytes, interfaces, micelles and enzymes, can span several orders of magnitude in length and time scales. The length and time scales of processes occurring over this broad time and space window are frequently coupled to give rise to the control necessary to ensure specificity and the uniqueness of the chemical phenomena. A combination of experimental, theoretical and computational techniques that can address a multiplicity of length and time scales is required in order to understand and predict structure and dynamics in such complex systems. This review highlights recent experimental developments that allow one to probe structure and dynamics at increasingly smaller length and time scales. The key theoretical approaches and computational strategies for integrating information across time-scales are discussed. The application of these ideas to understand phenomena in various areas, ranging from materials science to biology, is illustrated in the context of current developments in the areas of liquids and solvation, protein folding and aggregation and phase transitions, nucleation and self-assembly.

Interplay of Virulence Factors in Complement Resistance of Streptococcus pneumoniae

Streptococcus pneumoniae (pneumococcus) is a normal inhabitant of the human nasopharynx. Symptoms occur in only a small proportion of those who become carriers, but the ubiquity of the organism in the human population results in a large burden of disease. S. pneumoniae is the leading bacterial cause of pneumonia, sepsis, and meningitis worldwide, causing the death of a million children each year. Middle-ear infection is the most common clinical manifestation of mucosal pneumococcal infections. In invasive disease, S. pneumoniae gains access to the bloodstream and spreads to normally sterile parts of the body. The progression from asymptomatic colonization to disease depends on factors characteristic of specific pneumococcal strains as well as the status of host defenses. The polysaccharide capsule surrounding the bacterium is considered to be the most important factor affecting the virulence of pneumococci. It protects pneumococci from phagocytosis and also may determine its affinity to the respiratory epithelium. S. pneumoniae as a species comprises more than 90 different capsular serotypes, but not all of them are equally prevalent in human diseases. Invasive serotypes are rarely isolated from healthy carriers, but relatively often cause invasive disease. Serotypes that are carried asymptomatically for a long time behave like opportunistic pathogens, causing disease in patients who have impaired immune defenses. The complement system is a collection of blood and cell surface proteins that act as a major primary defense against invading microbes. Phagocytic cells with receptors for complement proteins can engulf and destroy pneumococcal cells opsonized with these proteins. S. pneumoniae has evolved a number of ways to subvert mechanisms of innate immunity, and this is likely to contribute to its pathogenicity. The capsular serotype, proteins essential for virulence, as well the genotype, may all influence the ability of pneumococcus to resist complement and its potential to cause disease. Immunization with conjugate vaccines produces opsonic antibodies, which enhance complement deposition and clearance of the bacteria. The pneumococcal vaccine included in the Finnish national immunization program in 2010 contains the most common serotypes causing invasive disease. Clinical data suggest that protection from middle-ear infection and possibly also from invasive disease depends largely on the capsular serotype, for reasons hitherto unknown. The general aim of this thesis is to assess the relative roles of the pneumococcal capsule and virulence proteins in complement evasion and subsequent opsonophagocytic killing. The main question is whether differences between serotypes to resist complement explain the different abilities of serotypes to cause disease. The importance of particular virulence factors to the complement resistance of a strain may vary depending on its genotype. Prior studies have evaluated the effect of the capsule and virulence proteins on complement resistance of S. pneumoniae by comparing only a few strains. In this thesis, the role of pneumococcal virulence factors in the complement resistance of the bacterium was studied in several genotypically different strains. The ability of pneumococci to inhibit deposition of the complement protein C3 on the bacterial surface was found to depend on the capsular serotype as well as on other features of the bacteria. The results suggest that pneumococcal histidine triad (Pht) proteins may play a role in complement inhibition, but their contribution depends on the bacterial genotype. The capsular serotype was found to influence complement resistance more than the bacterial genotype. A higher concentration of anticapsular antibodies was required for the opsonophagocytic killing of serotypes resistant to C3 deposition. The invasive serotypes were more resistant to C3 deposition than the opportunistic serotypes, suggesting that the former are better adapted to resist immune mechanisms controlling the development of invasive disease. The different susceptibilities of serotypes to complement deposition, opsonophagocytosis, and resultant antibody-mediated protection should be taken into account when guidelines for serological correlates for vaccine efficacy evaluations are made. The results of this thesis suggest that antibodies in higher quantity or quality are needed for efficient protection against the invasive serotypes.

Studies of the Human Transcriptome

Gene expression is one of the most critical factors influencing the phenotype of a cell. As a result of several technological advances, measuring gene expression levels has become one of the most common molecular biological measurements to study the behaviour of cells. The scientific community has produced enormous and constantly increasing collection of gene expression data from various human cells both from healthy and pathological conditions. However, while each of these studies is informative and enlighting in its own context and research setup, diverging methods and terminologies make it very challenging to integrate existing gene expression data to a more comprehensive view of human transcriptome function. On the other hand, bioinformatic science advances only through data integration and synthesis. The aim of this study was to develop biological and mathematical methods to overcome these challenges and to construct an integrated database of human transcriptome as well as to demonstrate its usage. Methods developed in this study can be divided in two distinct parts. First, the biological and medical annotation of the existing gene expression measurements needed to be encoded by systematic vocabularies. There was no single existing biomedical ontology or vocabulary suitable for this purpose. Thus, new annotation terminology was developed as a part of this work. Second part was to develop mathematical methods correcting the noise and systematic differences/errors in the data caused by various array generations. Additionally, there was a need to develop suitable computational methods for sample collection and archiving, unique sample identification, database structures, data retrieval and visualization. Bioinformatic methods were developed to analyze gene expression levels and putative functional associations of human genes by using the integrated gene expression data. Also a method to interpret individual gene expression profiles across all the healthy and pathological tissues of the reference database was developed. As a result of this work 9783 human gene expression samples measured by Affymetrix microarrays were integrated to form a unique human transcriptome resource GeneSapiens. This makes it possible to analyse expression levels of 17330 genes across 175 types of healthy and pathological human tissues. Application of this resource to interpret individual gene expression measurements allowed identification of tissue of origin with 92.0% accuracy among 44 healthy tissue types. Systematic analysis of transcriptional activity levels of 459 kinase genes was performed across 44 healthy and 55 pathological tissue types and a genome wide analysis of kinase gene co-expression networks was done. This analysis revealed biologically and medically interesting data on putative kinase gene functions in health and disease. Finally, we developed a method for alignment of gene expression profiles (AGEP) to perform analysis for individual patient samples to pinpoint gene- and pathway-specific changes in the test sample in relation to the reference transcriptome database. We also showed how large-scale gene expression data resources can be used to quantitatively characterize changes in the transcriptomic program of differentiating stem cells. Taken together, these studies indicate the power of systematic bioinformatic analyses to infer biological and medical insights from existing published datasets as well as to facilitate the interpretation of new molecular profiling data from individual patients.

Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos

Represented by approximately 85 species, Hemidactylus is one of the most diverse and widely distributed genera of reptiles in the world. In the Indian subcontinent, this genus is represented by 28 species out of which at least 13 are endemic to this region. Here, we report the phylogeny of the Indian Hemidactylus geckos based on mitochondrial and nuclear DNA markers sequenced from multiple individuals of widely distributed as well as endemic congeners of India. Results indicate that a majority of the species distributed in India form a distinct clade whose members are largely confined to the Indian subcontinent thus representing a unique Indian radiation. The remaining Hemidactylus geckos of India belong to two other geographical clades representing the Southeast Asian and West-Asian arid zone species. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) are nested within the Indian radiation suggesting their Indian origin. Dispersal-vicariance analysis also supports their Indian origin and subsequent dispersal out-of-India into West-Asian arid zone and Southeast Asia. Thus, Indian subcontinent has served as an important arena for diversification amongst the Hemidactylus geckos and in the evolution and spread of its commensal geckos. (C) 2010 Elsevier Inc. All rights reserved.

Eu2+ luminescence in MAl3BO7 aluminoborates (M=Ca, Sr, Ba)

Three new aluminoborates having the composition MAl3BO7, where M = Ca,Sr or Ba, have been prepared. X-ray diffraction data indicate that all the phases are monoclinic, with close structural similarity to the meta stable aluminate, SrAl4O7. These aluminoborates are good host lattices for Eu2+ luminescence. The emission spectra show multiple bands in the blue region, corresponding to two inequivalent sites in each case, with one of them having quantum efficiency greater-than or equivalent to 75%. In the case of SrAl3BO7:Eu2+, the d–f band emission dominates at 300 K whereas at 77 K both d–f band and f–f line emissions are observed. Efficient Eu2+→Mn2+ energy transfer is observed in MAl3BO7 leading to strong green emission of Mn2+in the tetrahedral sites.aluminoborates; europium

Solution structure of BTK-2, a novel hK(v)1.1 inhibiting scorpion toxin, from the eastern Indian scorpion Mesobuthus tamulus

The three dimensional structure of a 32 residue three disulfide scorpion toxin, BTK-2, from the Indian red scorpion Mesobuthus tamulus has been determined using isotope edited solution NMR methods. Samples for structural and electrophysiological studies were prepared using recombinant DNA methods. Electrophysiological studies show that the peptide is active against hK(v)1.1 channels. The structure of BTK-2 was determined using 373 distance restraints from NOE data, 66 dihedral angle restraints from NOE, chemical shift and scalar coupling data, 6 constraints based on disulfide linkages and 8 constraints based on hydrogen bonds. The root mean square deviation (r.m.s.d) about the averaged co-ordinates of the backbone (N, C-alpha, C') and all heavy atoms are 0.81 +/- 0.23 angstrom and 1.51 +/- 0.29 angstrom respectively. The backbone dihedral angles (phi and psi) for all residues occupy the favorable and allowed regions of the Ramachandran map. The three dimensional structure of BTK-2 is composed of three well defined secondary structural regions that constitute the alpha-beta-beta, structural motif. Comparisons between the structure of BTK-2 and other closely related scorpion toxins pointed towards distinct differences in surface properties that provide insights into the structure-function relationships among this important class of voltage-gated potassium channel inhibiting peptides. (C) 2011 Elsevier B.V. All rights reserved.

Analysis of geometric and strain effects in homo-Diels-Alder reactions

Molecular mechanics calculations have been carried out to quantify the key geometric and strain effects which are likely to control the homo-Diels-Alder reactivity of 1,4-dienes. The criteria considered include C1..C5 and C2..C4 distances in the diene, twist angle of the two pi units, and the magnitude of strain increase as a result of cycloaddition. By first considering these factors in a number of non-conjugated dienes with known reactivity, the ranges of values within which the reaction is favoured are proposed. Calculations are also reported on several substrates which have not been investigated so far. Promising systems for experimental study are suggested which, in addition to being intrinsically interesting, would place the present proposals on a firm basis.

PC based integrated protection scheme for railway traction applications

This paper presents the design and development of a comprehensive digital protection scheme for applications in 25 KV a.c railway traction system. The scheme provides distance protection, detection of wrong phase coupling both in the lagging and leading directions, high set instantaneous trip and PT fuse failure. Provision is also made to include fault location and disturbance recording. The digital relaying scheme has been tried on two types of hardware platforms, one with PC/AT based hardware and the other with a custom designed standalone 16-bit microcontroller based card. Compared to the existing scheme, the operating time is around one cycle and the relaying algorithm has been optimised to minimise the number of computations. The prototype has been rigorously tested in the laboratory using a specially designed PC based relay test bench and the results are highly satisfactory.

Microwave Assisted Synthesis and Antimicrobial Study of Schiff Base Vanadium(IV) Complexes of Phenyl Esters of Amino Acids

Schiff base vanadium(IV) complexes of phenyl esters of the two acidic amino acids, i.e., aspartic and glutamic acid, were synthesized. The phenyl esters of these amino acids were synthesized by conventional method whereas the Schiff base vanadium(IV) complexes were synthesized using microwave irradiation. The complexes were characterized by spectroscopic tools such as IR, 1H NMR, mass (ES), ESR, and UV visible spectroscopy. All the complexes were studied for antibacterial and antifungal activity and found to be moderately active.

Swelling pressure of sodium montmorillonites

Determination of the swelling pressure of montmorillonitic clays is required in many situations concerned with stability problems of foundations, retaining walls, slope stability of embankments and excavations in expansive soils. Recently expansive soils such as bentonite have been used as a mixture backfill material, for example as backfill material for nuclear waste disposal systems, for which a knowledge of the swelling pressure is desirable. This is the pressure required to keep the clay-water system at the required void ratio when it is allowed to absorb water or electrolyte. If the pressure is less than the swelling pressure, volume expansion occurs; if the pressure is more than the swelling pressure, volume compression occurs. Because of isomorphous substitutions in the crystal lattice, in general the clay particles carry negative charges at the surfaces of the platelets. Exchangeable cations in the clay media are attracted to these negative charges, but this attraction is opposed by the tendency of ions to be distributed. As a result, an electric diffuse double layer is formed (Gouy, 1910).

Quantum phenomena in magnetic nano clusters

One of the fascinating fields of study in magnetism in recent years has been the study of quantum phenomena in nanosystems. While semiconductor structures have provided paradigms of nanosystems from the stand point of electronic phenomena the synthesis of high nuclearity transition metal complexes have provided examples of nano magnets. The range and diversity of the properties exhibited by these systems rivals its electronic counterparts. Qualitative understanding of these phenomena requires only a knowledge of basic physics, but quantitative study throws up many challenges that are similar to those encountered in the study of correlated electronic systems. In this article, a brief overview of the current trends in this area arc highlighted and some of the efforts of our group in developing a quantitative understanding of this field are outlined.

Water ingression and the role of interface on the compressive properties of epoxy filled with treated fly ash

Polymer composites are generally filled with either fibrous or particulate materials to improve the mechanical properties. In choosing the fillers one looks for materials that are inexpensive and available in abundance, in order to realize a cost reduction also. Also, often these fibres/fillers are treated to improve the matrix adhesion and thereby mechanical properties. The present study is focussed on the influence of water ingression in such filler-modified composites and the attendant changes in the compressive properties. The changes in property effected following exposure to aqueous media and the influence interface modification has on the scenario is emphasized in the work. It is seen that for plain epoxy and fly ash filled systems the strengths are increased following exposure to aqueous media. The composites with surface-treated ash particles, on the other hand, record a drop in the values. Modulus values show are increased to varying degree in unfilled and filled systems. The study also includes a fractographic analysis of the tested samples with and without exposure to water.

Effect of inorganic ions, H(2)O(2) and pH on the photocatalytic inactivation of Escherichia coli with silver impregnated combustion synthesized TiO(2) catalyst

The photocatalytic antibacterial activity of Ag impregnated combustion synthesized TiO(2) (0.25 g/L) was studied against Escherichia coil in presence of UV irradiation. The effect of various parameters, such as anions, canons, hydrogen peroxide and pH, on the photocatalytic inactivation was investigated. The addition of inorganic ions showed a negative effect on inactivation. Among anions, the presence of chloride ions was observed to have a maximum negative effect and reduced the inactivation considerably. Among cations, the bacterial inactivation reduced significantly in the presence of Ca(2+) ions. Hydrogen peroxide addition in combination with Ag/TiO(2) photocatalysis, however, improved the inactivation. Photocatalysis with high concentration of H(2)O(2) yielded complete bacterial inactivation within few minutes. The photocatalytic inactivation of E. coil was not affected by variation in pH. (C) 2011 Elsevier B.V. All rights reserved.