sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

Deformation and failure of a film/substrate system subjected to spherical indentation: Part 1. Experimental validation of stresses and strains derived using Hankel transform technique in an elastic film/substrate system

Our concern here is to rationalize experimental observations of failure modes brought about by indentation of hard thin ceramic films deposited on metallic substrates. By undertaking this exercise, we would like to evolve an analytical framework that can be used for designs of coatings. In Part I of the paper we develop an algorithm and test it for a model system. Using this analytical framework we address the issue of failure of columnar TiN films in Part II [J. Mater. Res. 21, 783 (2006)] of the paper. In this part, we used a previously derived Hankel transform procedure to derive stress and strain in a birefringent polymer film glued to a strong substrate and subjected to spherical indentation. We measure surface radial strains using strain gauges and bulk film stresses using photo elastic technique (stress freezing). For a boundary condition based on Hertzian traction with no film interface constraint and assuming the substrate constraint to be a function of the imposed strain, the theory describes the stress distributions well. The variation in peak stresses also demonstrates the usefulness of depositing even a soft film to protect an underlying substrate.

Direct detection of atmospheric particle formation using the Neutral cluster and Air Ion Spectrometer

Aerosol particles play an important role in the Earth s atmosphere and in the climate system: they scatter and absorb solar radiation, facilitate chemical processes, and serve as seeds for cloud formation. Secondary new particle formation (NPF) is a globally important source of these particles. Currently, the mechanisms of particle formation and the vapors participating in this process are, however, not truly understood. In order to fully explain atmospheric NPF and subsequent growth, we need to measure directly the very initial steps of the formation processes. This thesis investigates the possibility to study atmospheric particle formation using a recently developed Neutral cluster and Air Ion Spectrometer (NAIS). First, the NAIS was calibrated and intercompared, and found to be in good agreement with the reference instruments both in the laboratory and in the field. It was concluded that NAIS can be reliably used to measure small atmospheric ions and particles directly at the sizes where NPF begins. Second, several NAIS systems were deployed simultaneously at 12 European measurement sites to quantify the spatial and temporal distribution of particle formation events. The sites represented a variety of geographical and atmospheric conditions. The NPF events were detected using NAIS systems at all of the sites during the year-long measurement period. Various particle formation characteristics, such as formation and growth rates, were used as indicators of the relevant processes and participating compounds in the initial formation. In a case of parallel ion and neutral cluster measurements, we also estimated the relative contribution of ion-induced and neutral nucleation to the total particle formation. At most sites, the particle growth rate increased with the increasing particle size indicating that different condensing vapors are participating in the growth of different-sized particles. The results suggest that, in addition to sulfuric acid, organic vapors contribute to the initial steps of NPF and to the subsequent growth, not just later steps of the particle growth. As a significant new result, we found out that the total particle formation rate varied much more between the different sites than the formation rate of charged particles. The results infer that the ion-induced nucleation has a minor contribution to particle formation in the boundary layer in most of the environments. These results give tools to better quantify the aerosol source provided by secondary NPF in various environments. The particle formation characteristics determined in this thesis can be used in global models to assess NPF s climatic effects.

Designing Creativity Through Clusters - A periodisation of cluster discourse

The thesis focuses on one of the most dominant articulations of the relation between geographical place and development, clusters - internationally competing place-bound economic system of production in related industries. The dominant articulation of cluster discourse represents the subnational region as a system of production, and as a means for competitiveness for Western countries. Its reproduction in theories has become one of the most prolific exports of economic geography to other disciplines and for policymaking. By analysing cluster discourse the thesis traces how the languages and processes of globalization have over time altered the understandings of the relation between geographical place and the economy. It shows how in its latest incarnation of the cluster discourse, the language of mainstream economics is combined with ‘softer’ elements (e.g. community, learning, creativity) in the economic geographic discourse. This is typical for the idea of soft capitalism, wherein it is assumed that economic success emanates from soft characteristics, such as knowledge, learning and creativity, rather than straightforward technological or cost advantages. A reoccurring critique against the dominant understanding of the relationship between competitiveness and regions, as articulated in cluster discourse, has pinpointed the perspective’s inability to reconcile the respective and reciprocal roles of local standard of living with firm competitiveness. The thesis traces how such critique is increasingly appropriated through the fusion of the economic, social and cultural landscape into the language of capitalism. It shows how cluster discourse has appropriated its critique, by focusing on creativity, with its strong associations to arts, individual artists and the cultural sphere in general, while predominantly creating its meaning in relation to competitiveness. The thesis consists of six essays that each outlines the development of the cluster discourse. The essays show how meaning systems and strategies are created, accepted and naturalized in cluster discourse, how this affects individuals, the economic landscape and society at large, as well as showing which understandings are marginalized in the process. The thesis argues that clusters are a) inseparable from ideology and politics and b) they are the result of purposeful social practice. It calls for increased reflexivity within corporate and economic geographic research on clusters, and underlines the importance of placing issues of power at the centre of analysis.

Synthesis, structure and magnetic properties of the polyoxovanadate cluster Zn-2(NH2(CH2)(2)NH2)(5)]{Zn(NH2(CH2)(2)NH2)(2)}(2){V18O42(H2O)\ ]center dot xH(2)O (x similar to 12), possessing a layered structure

A hydrothermal reaction of a mixture of ZnCl2, V2O5, ethylenediamine and water gave rise to a layered poly oxovanadate material. clusters. These clusters, with all the vanadium ions in the +4 state, are connected together through Zn(NH2(CH2)(2)NH2)(2) linkers forming a two-dimensional structure. The layers are also separated by distorted trigonal bipyramidal [Zn-2(NH2(CH2)(2)NH2)(5)] complexes. The Structure, thus, presents a dual role for the Zn-ethylenediamine complex. The magnetic susceptibility studies indicate that the interactions between the V centres in I are predominantly antiferromagnetic in nature and the compound shows highly frustrated behaviour. The magnetic properties are compared to the theoretical calculations based oil the Heisenberg model, in addition to correlating to the structure. Crystal data for the complexes are presented.

Synthesis and characterization of Ti5Te4-type molybdenum cluster compounds, AxMo5As4(A = Cu, Al, or Ga)

A new series of molybdenum cluster compounds of the general formula AxMo5As4(A = Cu, Al, or Ga) has been synthesized. They are isostructural with the host Mo5As4(Ti5Te4-type) consisting of trans-vertex shared Mo6 octahedral chains. Investigations by X-ray photoelectron and Auger electron spectroscopies revealed a charge transfer from A to Mo5As4 in AxMo5As4. The occurrence of metallic (CuxMo5As4) and non-metallic (Al2Mo5As4 and Ga2Mo5As4) properties in this isostructural series of solids is consistent with the electronic structure of Ti5Te4-type solids involving M–M bonding in the cluster chains.

Synthesis and characterization of Pd(0), PdS, and Pd@PdO core-shell nanoparticles by solventless thermolysis of a Pd-thiolate cluster

Colloids of palladium nanoparticles have been prepared by the solvated metal atom dispersion (SMAD) method. The as-prepared Pd colloid consists of particles with an average diameter of 2.8 +/- 0.1 nm. Digestive ripening of the as-prepared Pd colloid, a process involving refluxing the as-prepared colloid at or near the boiling point of the solvent in the presence of a passivating agent, dodecanethiol resulted in a previously reported Pd-thiolate cluster, Pd(SC12H25)(2)](6) but did not render the expected narrowing down of the particle size distribution. Solventless thermolysis of the Pd-thiolate complex resulted in various Pd systems such as Pd(0), PdS, and Pd@PdO core-shell nanoparticles thus demonstrating its versatility. These I'd nanostructures have been characterized using high-resolution electron microscopy and powder X-ray diffraction methods. (C) 2010 Elsevier Inc. All rights reserved.

H I deficiency in cluster spiral galaxies - Dependence on galaxy size

From the available H I data on spiral galaxies in three rich Abell clusters and the Virgo Cluster, it is shown that galaxies with medium to large optical sizes tend to be more severely deficient in atomic hydrogen than the small galaxies. This is so both in terms of the fractional number of galaxies that are deficient and the amount of gas lost by a galaxy. The fraction of H I-deficient galaxies increases with size over most of the size range, saturating or dropping only for the largest galaxies. A comparative study is made of various currently accepted gas removal mechanisms, namely those which are a result of galaxy-intracluster medium interactions, e.g., ram pressure stripping, as well as those due to galaxy-galaxy interactions, i.e., collisions and tidal interactions. It is shown that, with the exception of tidal interactions, all of these mechanisms would produce a size dependence in H I deficiency that is the opposite of that observed. That is, the gas in the largest galaxies would be the least affected by these mechanisms. However, if there is significant mass segregation, these processes may give the trends observed in the size dependence of H I deficiency.

Categorical Meteorological Products: Evaluation and Analysis

In meteorology, observations and forecasts of a wide range of phenomena for example, snow, clouds, hail, fog, and tornados can be categorical, that is, they can only have discrete values (e.g., "snow" and "no snow"). Concentrating on satellite-based snow and cloud analyses, this thesis explores methods that have been developed for evaluation of categorical products and analyses. Different algorithms for satellite products generate different results; sometimes the differences are subtle, sometimes all too visible. In addition to differences between algorithms, the satellite products are influenced by physical processes and conditions, such as diurnal and seasonal variation in solar radiation, topography, and land use. The analysis of satellite-based snow cover analyses from NOAA, NASA, and EUMETSAT, and snow analyses for numerical weather prediction models from FMI and ECMWF was complicated by the fact that we did not have the true knowledge of snow extent, and we were forced simply to measure the agreement between different products. The Sammon mapping, a multidimensional scaling method, was then used to visualize the differences between different products. The trustworthiness of the results for cloud analyses [EUMETSAT Meteorological Products Extraction Facility cloud mask (MPEF), together with the Nowcasting Satellite Application Facility (SAFNWC) cloud masks provided by Météo-France (SAFNWC/MSG) and the Swedish Meteorological and Hydrological Institute (SAFNWC/PPS)] compared with ceilometers of the Helsinki Testbed was estimated by constructing confidence intervals (CIs). Bootstrapping, a statistical resampling method, was used to construct CIs, especially in the presence of spatial and temporal correlation. The reference data for validation are constantly in short supply. In general, the needs of a particular project drive the requirements for evaluation, for example, for the accuracy and the timeliness of the particular data and methods. In this vein, we discuss tentatively how data provided by general public, e.g., photos shared on the Internet photo-sharing service Flickr, can be used as a new source for validation. Results show that they are of reasonable quality and their use for case studies can be warmly recommended. Last, the use of cluster analysis on meteorological in-situ measurements was explored. The Autoclass algorithm was used to construct compact representations of synoptic conditions of fog at Finnish airports.

Structure of a cyclic water tetramer in a nucleotide crystal host and a hypothetical model for water cluster growth

Structure of a cyclic water tetramer in channels (pores) formed by self-assembly of N6-methyl-5'-AMP center dot Na-2 molecules is described and a hypothetical model is proposed for growth of water clusters. (C) 2010 Elsevier B.V. All rights reserved.

Activation barriers for d.c. conductivity in ionic glasses: Classical calculations using the small-cluster approximation

A small-cluster approximation has been used to calculate the activation barriers for the d.c. conductivity in ionic glasses. The main emphasis of this approach is on the importance of the hitherto ignored polarization energy contribution to the total activation energy. For the first time it has been demonstrated that the d.c. conductivity activation energy can be calculated by considering ionic migration to a neighbouring vacancy in a smali cluster of ions consisting of face-sharing anion polyhedra. The activation energies from the model calculations have been compared with the experimental values in the case of highly modified lithium thioborate glasses.

Compressive tidal heating of a disk galaxy in a rich cluster

The restricted three-body method is used to model the effect of the mean tidal field of a cluster of galaxies on the internal dynamics of a disk galaxy falling into the cluster for the first time. In the model adopted the galaxy experiences a tidal field that is compressive within the core of the cluster. The planar random velocities of all components in the disk increase after the galaxy passes through the core of the cluster. The low-velocity dispersion gas clouds experience a relatively larger increase in random velocity than the hotter stellar components. The increase in planar velocities results in a strong anisotropy between the planar and vertical velocity dispersions. It is argued that this will make the disk unstable to the 'fire-hose instability' which leads to bending modes in the disk and which will thicken the disk slightly. The mean tidal fields in rich clusters were probably stronger during the epoch of cluster formation and relaxation than they are in present-day relaxed clusters.

Effect of Sorbate-Zeolite Interaction on Cluster Lifetime and Size of Sorbates: Xe in NaY

Molecular dynamics calculations are reported for Xe in sodium Y zeolite with varying strengths of sorbate-zeolite dispersion interaction. In the absence of any dispersion interaction between the sorbate and the zeolite, the presence of the zeolite has a purely geometrical role. Increase in the strength of the sorbate-zeolite interaction increases the monomer population and decreases the population of dimers and higher sized clusters. The lifetime of the monomers as well as dimers increases with the strength of the dispersion interaction. The observed variations in the lifetime and the population of the different sized clusters is explained in terms of the changes in the potential energy surface caused by the increase in the strength of the dispersion interaction.