Tuning nuclearity of clusters by positional change of functional group: Synthesis of polynuclear clusters, crystal structures and magnetic properties

Four neutral polynuclear magnetic clusters, (Mn6Mn2Na2I)-Mn-III-Na-II(N-3)(8)(mu(1)-O)(2)(L-1)(6)(CH3OH)(2)] (1), (Mn6Na2I)-Na-III(N-3)(4)(mu(4)-O)(2)(L-2)(4)(CH3COO)(4)] (2), Ni-5(II)(N-3)(4)(HL1)(4)(HCOO)(2)(CH3OH)(2)(H2O)(2)]center dot 2CH(3)OH (3) and (Ni4Na2I)-Na-II(N-3)(4)(HL2)(6)]center dot 2CH(3)OH (4) have been synthesized using tetradentate ligands H2L1-2 along with azide as a co-ligand. H2L1-2 are the products formed in situ upon condensation of 2-hydroxy-3-methoxybenzaldehyde with 1-aminopropan-2-ol and 1-aminopropan-3-ol, respectively. Single crystal X-ray diffraction and bond valence sum calculation showed that complex 1 is composed of both Mn-III and Mn-II. Complex 3 contains coordinated formate, which was formed upon in situ oxidation of methanol. The magnetic study over a wide range of temperatures of all the complexes (1-4) showed that 1 and 2 are antiferromagnetic whereas other two (3-4) are predominantly ferromagnetic. The estimated ground states of the complexes are S approximate to 3(1), S = 4(2), S = 5(3) and S approximate to 4(4), respectively. (C) 2014 Elsevier B.V. All rights reserved.

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Multi-Temporal Satellite Image Analysis Using Gene Expression Programming

This paper discusses an approach for river mapping and flood evaluation to aid multi-temporal time series analysis of satellite images utilizing pixel spectral information for image classification and region-based segmentation to extract water covered region. Analysis of Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images is applied in two stages: before flood and during flood. For these images the extraction of water region utilizes spectral information for image classification and spatial information for image segmentation. Multi-temporal MODIS images from ``normal'' (non-flood) and flood time-periods are processed in two steps. In the first step, image classifiers such as artificial neural networks and gene expression programming to separate the image pixels into water and non-water groups based on their spectral features. The classified image is then segmented using spatial features of the water pixels to remove the misclassified water region. From the results obtained, we evaluate the performance of the method and conclude that the use of image classification and region-based segmentation is an accurate and reliable for the extraction of water-covered region.

Clusters, asters, and collective oscillations in chemotactic colloids

The creation of synthetic systems that emulate the defining properties of living matter, such as motility, gradient-sensing, signaling, and replication, is a grand challenge of biomimetics. Such imitations of life crucially contain active components that transform chemical energy into directed motion. These artificial realizations of motility point in the direction of a new paradigm in engineering, through the design of emergent behavior by manipulating properties at the scale of the individual components. Catalytic colloidal swimmers are a particularly promising example of such systems. Here we present a comprehensive theoretical description of gradient-sensing of an individual swimmer, leading controllably to chemotactic or anti-chemotactic behavior, and use it to construct a framework for studying their collective behavior. We find that both the positional and the orientational degrees of freedom of the active colloids can exhibit condensation, signaling formation of clusters and asters. The kinetics of catalysis introduces a natural control parameter for the range of the interaction mediated by the diffusing chemical species. For various regimes in parameter space in the long-ranged limit our system displays precise analogs to gravitational collapse, plasma oscillations, and electrostatic screening. We present prescriptions for how to tune the surface properties of the colloids during fabrication to achieve each type of behavior.

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films

Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-beta and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation. Published by Elsevier Ltd.

Cu-II-Azide Polynuclear Complexes of Three Different Building Clusters with the Same Schiff-Base Ligand: Synthesis, Structures, Magnetic Behavior, and Density Functional Theory Studies

Three copper-azido complexes Cu-4(N-3)(8)(L-1)(2)(MeOH)(2)](n) (1), Cu-4(N-3)(8)(L-1)(2)] (2), and Cu-5(N-3)(10)(L-1)(2)](n) (3) L-1 is the imine resulting from the condensation of pyridine-2-carboxaldehyde with 2-(2-pyridyl)ethylamine] have been synthesized using lower molar equivalents of the Schiff base ligand with Cu(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single crystal X-ray structures show that the basic unit of the complexes 1 and 2 contains Cu-4(II) building blocks; however, they have distinct basic and overall structures due to a small change in the bridging mode of the peripheral pair of copper atoms in the linear tetranudear structures. Interestingly, these changes are the result of changing the solvent system (MeOH/H2O to EtOH/H2O) used for the synthesis, without changing the proportions of the components (metal to ligand ratio 2:1). Using even lower proportions of the ligand, another unique complex was isolated with Cu-5(II) building units, forming a two-dimensional complex (3). Magnetic susceptibility measurements over a wide range of temperature exhibit the presence of both antiferromagnetic (very weak) and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional, and two different basis sets) have been performed on the complexes 1 and 2 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

Designing stuffed hetero-fullerene nano-clusters: C26B46N12 and C14B58N12Li12

The stuffed fullerene-like nano clusters based on the approximately spherical B-84, (B-12@B-12@B-60, fragment of the beta-rhombohedral boron), are proposed using Wade's Rules and the criterion of overlap matching. Thus the fifty additional electrons required to make the B-84 skeleton electron sufficient, are provided by replacing 26 boron atoms by carbon atoms and 12 boron atoms by nitrogen atoms giving rise to C26B46N12. This particular combination has the added advantage of the fullerene surface made from C2B3N five-membered rings having less strain arising from the pyramidalization of the sp(2) hybridised trigonal planar carbon or nitrogen; the natural angle needed to have an optimum overlap is not far from the 31.7 degrees required for icosahedral symmetry. The advantage from overlap-matching can be further increased by capping the two pentagonal faces of the cluster by a Li atom each, keeping the electron count the same by replacing 12 carbon atoms with 12 boron atoms. DFT based computational results support these formulations.

Methylation Silencing of ULK2, an Autophagy Gene, Is Essential for Astrocyte Transformation and Tumor Growth

Glioblastoma (GBM) is the most aggressive type of brain tumor and shows very poor prognosis. Here, using genome-wide methylation analysis, we show that G-CIMP+ and G-CIMP-subtypes enrich distinct classes of biological processes. One of the hypermethylated genes in GBM, ULK2, an upstream autophagy inducer, was found to be down-regulated in GBM. Promoter hypermethylation of ULK2 was confirmed by bisulfite sequencing. GBM and glioma cell lines had low levels of ULK2 transcripts, which could be reversed upon methylation inhibitor treatment. ULK2 promoter methylation and transcript levels showed significant negative correlation. Ectopic overexpression of ULK2-induced autophagy, which further enhanced upon nutrient starvation or temozolomide chemotherapy. ULK2 also inhibited the growth of glioma cells, which required autophagy induction as kinase mutant of ULK2 failed to induce autophagy and inhibit growth. Furthermore, ULK2 induced autophagy and inhibited growth in Ras-transformed immortalized Baby Mouse Kidney (iBMK) ATG5(+/+) but not in autophagy-deficient ATG5(-/-) cells. Growth inhibition due to ULK2 induced high levels of autophagy under starvation or chemotherapy utilized apoptotic cell death but not at low levels of autophagy. Growth inhibition by ULK2 also appears to involve catalase degradation and reactive oxygen species generation. ULK2 overexpression inhibited anchorage independent growth, inhibited astrocyte transformation in vitro and tumor growth in vivo. Of all autophagy genes, we found ULK2 and its homologue ULK1 were only down-regulated in all grades of glioma. Thus these results altogether suggest that inhibition of autophagy by ULK1/2 down-regulation is essential for glioma development.

A Novel Mutation in the Transglutaminase-1 Gene in an Autosomal Recessive Congenital Ichthyosis Patient

Structure-function implication on a novel homozygous Trp250/Gly mutation of transglutaminase-1 (TGM1) observed in a patient of autosomal recessive congenital ichthyosis is invoked from a bioinformatics analysis. Structural consequences of this mutation are hypothesized in comparison to homologous enzyme human factor XIIIA accepted as valid in similar structural analysis and are projected as guidelines for future studies at an experimental level on TGM1 thus mutated.

Co-liposomes comprising a lipidated multivalent RGD-peptide and a cationic gemini cholesterol induce selective gene transfection in alpha v beta 3 and alpha v beta 5 integrin receptor-rich cancer cells

The alpha v beta 3 and alpha v beta 5 integrins, transmembrane glycoprotein receptors, are over-expressed in numerous tumors and in endothelial cells that constitute tumor blood vessels. As this protein selectively binds to the Arg-Gly-Asp (RGD) sequence containing peptides, it is an attractive way to target tumors. Herein we have developed novel formulations for integrin mediated selective gene delivery. These formulations are composed of a novel palmitoylated tetrameric RGD containing scaffold (named RAFT-RGD), cationic gemini cholesterol (GL5) and a natural helper lipid 1,2-dioleoyl-L-alpha-glycero-3-phosphatidylethanolamine (DOPE). We have optimized a co-liposomal formulation to introduce the multivalent RGD-containing macromolecule in GL5: DOPE (GL5D) mixture to produce GL5D-RGD. We have unambiguously shown the selectivity of these formulations towards cancer cells that over express alpha v beta 3 and alpha v beta 5 integrins. Two reporter plasmids, pEGFP-C3 and PGL-3, were employed for the transfection experiments and it was shown that GL5D-RGD Liposomes increased exclusively the transfection in alpha v beta 3 and alpha v beta 5 overexpressing HeLa cells.