Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

Benzene carboxylic acids and Benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by H-1, C-13 and N-15 NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations. (C) 2012 Elsevier B.V. All rights reserved.

Natural Convection in a Vertical Channel with Arrays of Flush-Mounted Heaters on Opposite Conductive Walls

Three-dimensional numerical study of natural convection in a vertical channel with flush-mounted discrete heaters on opposite conductive substrate walls is carried out in the present work. Detailed flow and heat transfer characteristics are presented for various Grashof numbers. The heat transfer effects on one wall by the presence of heaters on its opposite wall is examined. It is found that heat transfer rates on one wall are increased by the presence of heaters on its opposite wall. The thermal boundary layers on the opposite walls complement each other for enhanced heat transfer. The effects of spacing between the heated walls, spacings between heaters and substrate conductivity on flow and heat transfer are examined. Existence of optimum spacings between the heated walls for maximum heat transfer and mass flow are observed. It is found that the heat transfer and fluid flow do not follow the same optimum spacings. Mass flow rate reaches maximum value at a wall spacing greater than the spacing for maximum heat transfer. This is because the interaction of thermal boundary layers on individual walls ceases at a lower spacing before the velocity boundary layers separate each other. It is found that increased spacings between heaters reduce individual heater temperatures provided the heaters close to exit on both substrates avail sufficient substrate potions on the exit side. Insufficient substrate portions between the exit heaters and the exit cause abnormal local temperature rise in the exit heaters which are the hottest ones among all the heaters. Optimal heater spacings exist for minimum hottest heater temperature rise. Correlations are presented for dimensionless mass flow rate, temperature maximum, and average Nusselt number.

Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation

Helicobacter pylori is an important human pathogen and one of the most successful chronic colonizers of the human body. H. pylori uses diverse mechanisms to modulate its interaction with the host in order to promote chronic infection and overcome host immune response. Restriction-modification genes are a major part of strain-specific genes present in H. pylori. The role of N-6 -adenine methylation in bacterial gene regulation and virulence is well established but not much is known about the effect of C-5 -cytosine methylation on gene expression in prokaryotes. In this study, it was observed by microarray analysis and RT-PCR, that deletion of an orphan C-5 -cytosine methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a significant effect on the expression of number of genes belonging to motility, adhesion and virulence. AM Delta DhpyAVIBM mutant strain has a different LPS profile and is able to induce high IL-8 production compared to wild-type. hpyAVIBM from strain 26695 is able to complement mutant SS1 and AM5 strains. This study highlights a possible significance of cytosine methylation in the physiology of H. pylori.

Synthesis dependent characteristics of Sr1-xMnxTiO3 (x=0.03, 0.05, 0.07 and 0.09)

Sr1-xMnxTiO3 (where x=0.03, 0.05, 0.07 and 0.09) was synthesized via different routes that include solid-state, oxalate precipitation and freeze drying. In oxalate precipitation technique, compositions corresponding to 3 and 5 mol% doping of Mn were monophasic whereas the higher compositions revealed the presence of the secondary phases such as MnO, Mn3O4 etc., as confirmed by high resolution X-ray diffraction (XRD) studies. The decomposition behavior of the precursors prepared using oxalate precipitation method corresponding to the above mentioned compositions was studied. Nanopowders of compositions pertaining to 5 to 9 mol% of Mn doping were obtained using freeze-drying technique. The average crystallite size of these nanopowders was found to be in the 35 to 65 nm range. The microstructural studies carried out on the sintered ceramics, fabricated using powders synthesized by different routes established the fine grained nature ( < 1 mu m) of the one obtained by freeze drying method. Raman scattering studies were carried out in order to complement the observations made from XRD regarding the phase purity. The dielectric properties of the ceramics obtained by different synthesis routes were studied in the 80-300 K temperature range at 100 kHz and the effect of grain size has been discussed. (C) 2012 Elsevier Inc. All rights reserved.

Salmonella enterica serovars Typhimurium and Typhi as model organisms Revealing paradigm of host-pathogen interactions

The lifestyle of intracellular pathogens has always questioned the skill of a microbiologist in the context of finding the permanent cure to the diseases caused by them. The best tool utilized by these pathogens is their ability to reside inside the host cell, which enables them to easily bypass the humoral immunity of the host, such as the complement system. They further escape from the intracellular immunity, such as lysosome and inflammasome, mostly by forming a protective vacuole-bound niche derived from the host itself. Some of the most dreadful diseases are caused by these vacuolar pathogens, for example, tuberculosis by Mycobacterium or typhoid fever by Salmonella. To deal with such successful pathogens therapeutically, the knowledge of a host-pathogen interaction system becomes primarily essential, which further depends on the use of a model system. A well characterized pathogen, namely Salmonella, suits the role of a model for this purpose, which can infect a wide array of hosts causing a variety of diseases. This review focuses on various such aspects of research on Salmonella which are useful for studying the pathogenesis of other intracellular pathogens.

Distinct Disulfide Isomers of mu-Conotoxins KIIIA and KIIIB Block Voltage-Gated Sodium Channels

In the preparation of synthetic conotoxins containing multiple disulfide bonds, oxidative folding can produce numerous permutations of disulfide bond connectivities. Establishing the native disulfide connectivities thus presents a significant challenge when the venom-derived peptide is not available, as is increasingly the case when conotoxins are identified from cDNA sequences. Here, we investigate the disulfide connectivity of mu-conotoxin KIIIA, which was predicted originally to have a C1-C9,C2-C15,C4-C16] disulfide pattern based on homology with closely related mu-conotoxins. The two major isomers of synthetic mu-KIIIA formed during oxidative folding were purified and their disulfide connectivities mapped by direct mass spectrometric collision-induced dissociation fragmentation of the disulfide-bonded polypeptides. Our results show that the major oxidative folding product adopts a C1-C15,C2-C9,C4-C16] disulfide connectivity, while the minor product adopts a C1-C16,C2-C9,C4-C15] connectivity. Both of these peptides were potent blockers of Na(v)1.2 (K-d values of 5 and 230 nM, respectively). The solution structure for mu-KIIIA based on nuclear magnetic resonance data was recalculated with the C1-C15,C2-C9,C4-C16] disulfide pattern; its structure was very similar to the mu-KIIIA structure calculated with the incorrect C1-C9,C2-C15,C4-C16] disulfide pattern, with an alpha-helix spanning residues 7-12. In addition, the major folding isomers of mu-KIIIB, an N-terminally extended isoform of mu-KIIIA, identified from its cDNA sequence, were isolated. These folding products had the same disulfide connectivities as mu-KIIIA, and both blocked Na(v)1.2 (K-d values of 470 and 26 nM, respectively). Our results establish that the preferred disulfide pattern of synthetic mu-KIIIA and mu-KIIIB folded in vitro is 1-5/2-4/3-6 but that other disulfide isomers are also potent sodium channel blockers. These findings raise questions about the disulfide pattern(s) of mu-KIIIA in the venom of Conus kinoshitai; indeed, the presence of multiple disulfide isomers in the venom could provide a means of further expanding the snail's repertoire of active peptides.

The Structural Characterization of Folded Peptides Containing the Conformationally Constrained beta-Amino Acid Residue beta(2,2)Ac(6)c

Backbone alkylation has been shown to result in a dramatic reduction in the conformational space that is sterically accessible to a-amino acid residues in peptides. By extension, the presence of geminal dialkyl substituents at backbone atoms also restricts available conformational space for beta and ? residues. Five peptides containing the achiral beta 2,2-disubstituted beta-amino acid residue, 1-(aminomethyl)cyclohexanecarboxylic acid (beta 2,2Ac6c), have been structurally characterized in crystals by X-ray diffraction. The tripeptide Boc-Aib-beta 2,2Ac6c-Aib-OMe (1) adopts a novel fold stabilized by two intramolecular H-bonds (C11 and C9) of opposite directionality. The tetrapeptide Boc-Aib-beta 2,2Ac6c]2-OMe (2) and pentapeptide Boc-Aib-beta 2,2Ac6c]2-Aib-OMe (3) form short stretches of a hybrid a beta C11 helix stabilized by two and three intramolecular H-bonds, respectively. The structure of the dipeptide Boc-Aib-beta 2,2Ac6c-OMe (5) does not reveal any intramolecular H-bond. The aggregation pattern in the crystal provides an example of an extended conformation of the beta 2,2Ac6c residue, forming a polar sheet like H-bond. The protected derivative Ac-beta 2,2Ac6c-NHMe (4) adopts a locally folded gauche conformation about the C beta?Ca bonds (?=-55.7 degrees). Of the seven examples of beta 2,2Ac6c residues reported here, six adopt gauche conformations, a feature which promotes local folding when incorporated into peptides. A comparison between the conformational properties of beta 2,2Ac6c and beta 3,3Ac6c residues, in peptides, is presented. Backbone torsional parameters of H-bonded a beta/beta a turns are derived from the structures presented in this study and earlier reports.

A regularized linear classifier for effective text classification

In document community support vector machines and naïve bayes classifier are known for their simplistic yet excellent performance. Normally the feature subsets used by these two approaches complement each other, however a little has been done to combine them. The essence of this paper is a linear classifier, very similar to these two. We propose a novel way of combining these two approaches, which synthesizes best of them into a hybrid model. We evaluate the proposed approach using 20ng dataset, and compare it with its counterparts. The efficacy of our results strongly corroborate the effectiveness of our approach.

On finding a set of healthy individuals from a large population

In this paper, we explore fundamental limits on the number of tests required to identify a given number of ``healthy'' items from a large population containing a small number of ``defective'' items, in a nonadaptive group testing framework. Specifically, we derive mutual information-based upper bounds on the number of tests required to identify the required number of healthy items. Our results show that an impressive reduction in the number of tests is achievable compared to the conventional approach of using classical group testing to first identify the defective items and then pick the required number of healthy items from the complement set. For example, to identify L healthy items out of a population of N items containing K defective items, when the tests are reliable, our results show that O(K(L - 1)/(N - K)) measurements are sufficient. In contrast, the conventional approach requires O(K log(N/K)) measurements. We derive our results in a general sparse signal setup, and hence, they are applicable to other sparse signal-based applications such as compressive sensing also.

Simultaneous measurement of mechanical and electrical contact resistances during nanoindentation of NiTi shape memory alloys

The nanoindentation technique can be employed in shape memory alloys (SMAs) to discern the transformation temperatures as well as to characterize their mechanical behavior. In this paper, we use it with simultaneous measurements of the mechanical and the electrical contact resistances (ECR) at room temperature to probe two SMAs: austenite (RTA) and martensite (RTM). Two different types of indenter tips - Berkovich and spherical - are employed to examine the SMAs' indentation responses as a function of the representative strain, epsilon(R). In Berkovich indentation, because of the sharp nature of the tip, and in consequence the high levels of strain imposed, discerning the two SMAs on the basis of the indentation response alone is difficult. In the case of the spherical tip, epsilon(R) is systematically varied and its effect on the depth recovery ratio, eta(d), is examined. Results indicate that RTA has higher eta(d) than RTM, but the difference decreases with increasing epsilon(R) such that eta(d) values for both the alloys would be similar in the fully plastic regime. The experimental trends in eta(d) vs. epsilon(R) for both the alloys could be described well with a eta(d) proportional to (epsilon(R))(-1) type equation, which is developed on the basis of a phenomenological model. This fit, in turn, directs us to the maximum epsilon(R), below which plasticity underneath the indenter would not mask the differences in the two SMAs. It was demonstrated that the ECR measurements complement the mechanical measurements in demarcating the reverse transformation from martensite to austenite during unloading of RTA, wherein a marked increase in the voltage was noted. A correlation between recovery due to reverse transformation during unloading and increase in voltage (and hence the electrical resistance) was found. (C) 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

On k-stellated and k-stacked spheres

We introduce the class Sigma(k)(d) of k-stellated (combinatorial) spheres of dimension d (0 <= k <= d + 1) and compare and contrast it with the class S-k(d) (0 <= k <= d) of k-stacked homology d-spheres. We have E-1(d) = S-1(d), and Sigma(k)(d) subset of S-k(d) ford >= 2k-1. However, for each k >= 2 there are k-stacked spheres which are not k-stellated. For d <= 2k - 2, the existence of k-stellated spheres which are not k-stacked remains an open question. We also consider the class W-k(d) (and K-k(d)) of simplicial complexes all whose vertex-links belong to Sigma(k)(d - 1) (respectively, S-k(d - 1)). Thus, W-k(d) subset of K-k(d) for d >= 2k, while W-1(d) = K-1(d). Let (K) over bar (k)(d) denote the class of d-dimensional complexes all whose vertex-links are k-stacked balls. We show that for d >= 2k + 2, there is a natural bijection M -> (M) over bar from K-k(d) onto (K) over bar (k)(d + 1) which is the inverse to the boundary map partial derivative: (K) over bar (k)(d + 1) -> (K) over bar (k)(d). Finally, we complement the tightness results of our recent paper, Bagchi and Datta (2013) 5], by showing that, for any field F, an F-orientable (k + 1)-neighbourly member of W-k(2k + 1) is F-tight if and only if it is k-stacked.

N-Terminal disordered domain of saccharomyces cerevisiae Hop1 protein Is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is ecessary for spore formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.

Integrating biodiversity and conservation with modern agricultural landscapes

To achieve food security and meet the demands of the ever-growing human populations, farming systems have assumed unsustainable practices to produce more from a finite land area. This has been cause for concern mainly due to the often-irreversible damage done to the otherwise productive agricultural landscapes. Agro-ecology is proclaimed to be deteriorating due to eroding integrity of connected ecological mosaics and vulnerability to climate change. This has contributed to declining species diversity, loss of buffer vegetation, fragmentation of habitats, and loss of natural pollinators or predators, which eventually leads to decline in ecosystem services. Currently, a hierarchy of conservation initiatives is being considered to restore ecological integrity of agricultural landscapes. However, the challenge of identifying a suitable conservation strategy is a daunting task in view of socio-ecological factors that may constrain the choice of available strategies. One way to mitigate this situation and integrate biodiversity with agricultural landscapes is to implement offset mechanisms, which are compensatory and balancing approaches to restore the ecological health and function of an ecosystem. This needs to be tailored to the history of location specific agricultural practices, and the social, ecological and environmental conditions. The offset mechanisms can complement other initiatives through which farmers are insured against landscape-level risks such as droughts, fire and floods. For countries in the developing world with significant biodiversity and extensive agriculture, we should promote a comprehensive model of sustainable agricultural landscapes and ecosystem services, replicable at landscape to regional scales. Arguably, the model can be a potential option to sustain the integrity of biodiversity mosaic in agricultural landscapes.

Sustaining cooperation on networks: an analytical study based on evolutionary game theory

We analytically study the role played by the network topology in sustaining cooperation in a society of myopic agents in an evolutionary setting. In our model, each agent plays the Prisoner's Dilemma (PD) game with its neighbors, as specified by a network. Cooperation is the incumbent strategy, whereas defectors are the mutants. Starting with a population of cooperators, some agents are switched to defection. The agents then play the PD game with their neighbors and compute their fitness. After this, an evolutionary rule, or imitation dynamic is used to update the agent strategy. A defector switches back to cooperation if it has a cooperator neighbor with higher fitness. The network is said to sustain cooperation if almost all defectors switch to cooperation. Earlier work on the sustenance of cooperation has largely consisted of simulation studies, and we seek to complement this body of work by providing analytical insight for the same. We find that in order to sustain cooperation, a network should satisfy some properties such as small average diameter, densification, and irregularity. Real-world networks have been empirically shown to exhibit these properties, and are thus candidates for the sustenance of cooperation. We also analyze some specific graphs to determine whether or not they sustain cooperation. In particular, we find that scale-free graphs belonging to a certain family sustain cooperation, whereas Erdos-Renyi random graphs do not. To the best of our knowledge, ours is the first analytical attempt to determine which networks sustain cooperation in a population of myopic agents in an evolutionary setting.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.