Quorum Sensing and Biofilm Formation in Mycobacteria: Role of c-di-GMP and Methods to Study This Second Messenger

Bacteria have evolved to survive the ever-changing environment using intriguing mechanisms of quorum sensing (QS). Very often, QS facilitates formation of biofilm to help bacteria to persist longer and the formation of such biofilms is regulated by c-di-GMP. It is a well-known second messenger also found in mycobacteria. Several methods have been developed to study c-di-GMP signaling pathways in a variety of bacteria. In this review, we have attempted to highlight a connection between c-di-GMP and biofilm formation and QS in mycobacteria and several methods that have helped in better understanding of c-di-GMP signaling. (c) 2014 IUBMB Life, 66(12):823-834, 2014

Chemical Functionalization of Graphene To Augment Stem Cell Osteogenesis and Inhibit Biofilm Formation on Polymer Composites for Orthopedic Applications

Toward designing the next generation of resorbable biomaterials for orthopedic applications, we studied poly(epsilon-caprolactone) (PCL) composites containing graphene. The role, if any, of the functionalization of graphene on mechanical properties, stem cell response, and biofilm formation was systematically evaluated. PCL composites of graphene oxide (GO), reduced GO (RGO), and amine-functionalized GO (AGO) were prepared at different filler contents (1%, 3%, and 5%). Although the addition of the nanoparticles to PCL markedly increased the storage modulus, this increase was largest for GO followed by AGO and RGO. In vitro cell studies revealed that the AGO and GO particles significantly increased human mesenchymal stem cell proliferation. AGO was most effective in augmenting stem cell osteogenesis leading to mineralization. Bacterial studies revealed that interaction with functionalized GO induced bacterial cell death because of membrane damage, which was further accentuated by amine groups in AGO. As a result, AGO composites were best at inhibiting biofilm formation. The synergistic effect of oxygen containing functional groups and amine groups on AGO imparts the optimal combination of improved modulus, favorable stem cell response, and biofilm inhibition in AGO-reinforced composites desired for orthopedic applications. This work elucidates the importance of chemical functionalization of graphene in polymer composites for biomedical applications.

Synthesis, luminescence properties and EPR investigation of hydrothermally derived uniform ZnO hexagonal rods

One-dimensional (1D) zinc oxide (ZnO) hexagonal rods have been successfully synthesized by surfactant free hydrothermal process at different temperatures. It can be found that the reaction temperature play a crucial role in the formation of ZnO uniform hexagonal rods. The possible formation processes of 1-D ZnO hexagonal rods were investigated. The zinc hydroxide acts as the morphology-formative intermediate for the formation of ZnO nanorods. Upon excitation at 325 nm, the sample prepared at 180 degrees C show several emission bands at 400 nm (similar to 3.10 eV), 420 nm (similar to 2.95 eV), 482 nm (similar to 2.57 eV) and 524 nm (similar to 2.36 eV) corresponding to different kind of defects. TL studies were carried out by pre-irradiating samples with gamma-rays ranging from 1 to 7 kGy at room temperature. A well resolved glow peak at similar to 354 degrees C was recorded which can be ascribed to deep traps. Furthermore, the defects associated with surface states in ZnO nano-structures are characterized by electron paramagnetic resonance. (C) 2014 Elsevier B.V. All rights reserved.

Differential response of cholesterol based pyrimidine systems with oxyethylene type spacers to gelation and mesogen formation in the presence of alkali metal ions

A new series of lipophilic cholesteryl derivatives of 2,4,6-trichloro-pyrimidine-5-carbaldehyde has been synthesized. Oxyethylene spacers of variable lengths were inserted between the hydrogen bonding promoting pyrimidine core and the cholesteryl tail in order to understand their effect on the selfassembly of these compounds. Only compound 1a with the shortest spacer formed a gel in organic solvents such as n-butanol and n-dodecane. While other members (1b and c) having longer spacers led to sol formation and precipitation in n-butanol and n-dodecane respectively. The self-assembly phenomena associated with the gelation process were investigated using temperature-dependent UVVis and CD-spectroscopy. The morphological features of the freeze-dried gels obtained from different organic solvents were examined by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The solid phase behaviours of these molecules and their associated alkali metal ion complexes were explored using polarized optical microscopy (POM) and differential scanning calorimetry (DSC). The molecular arrangements in the xerogel and in the solid state were further probed using a wide-angle Xray diffraction (WAXD) technique. Analysis of the wide-angle X-ray diffraction data reveals that this class of molecules adopts a hexagonal columnar organization in the gel and in the solid state. Each slice of these hexagonal columnar structures is composed of a dimeric molecular-assembly as a building block. Significant changes in the conformation of the oxyethylene chains could be triggered via the coordination of selected alkali metal ions. This led to the production of interesting metal ion promoted mesogenic behaviour.

Charge Transfer Induces Formation of Stimuli-Responsive, Chiral, Cohesive Vesicles-on-a-String that Eventually Turn into a Hydrogel

A charge transfer (CT) mediated two-component, multistimuli responsive supergelation involving a L-histidine-appended pyrenyl derivative (PyHisOMe) as a donor and an asymmetric bolaamphiphilic naphthalene-diimide (Asym-NDI) derivative as an acceptor in a 2: 1 mixture of H2O/MeOH was investigated. Asym-NDI alone self-assembled into pH-responsive vesicular nanostructures in water. Excellent selectivity in CT gel formation was achieved in terms of choosing amino acid appended pyrenyl donor scaffolds. Circular di-chroism and morphological studies suggested formation of chiral, interconnected vesicular assemblies resembling ``pearls-on-a-string'' from these CT mixed stacks. XRD studies revealed the formation of monolayer lipid membranes from these CT mixed stacks that eventually led to the formation of individual vesicles. Strong cohesive forces among the interconnected vesicles originate from the protrusion of the oxyethylene chains from the surfaces of the chiral vesicles.

Formation of Prestellar Cores via Non-Isothermal Gas Fragmentation

Sheet-like clouds are common in turbulent gas and perhaps form via collisions between turbulent gas flows. Having examined the evolution of an isothermal shocked slab in an earlier contribution, in this work we follow the evolution of a sheet-like cloud confined by (thermal) pressure and gas in it is allowed to cool. The extant purpose of this endeavour is to study the early phases of core-formation. The observed evolution of this cloud supports the conjecture that molecular clouds themselves are three-phase media (comprising viz. a stable cold and warm medium, and a third thermally unstable medium), though it appears, clouds may evolve in this manner irrespective of whether they are gravitationally bound. We report, this sheet fragments initially due to the growth of the thermal instability (TI) and some fragments are elongated, filament-like. Subsequently, relatively large fragments become gravitationally unstable and sub-fragment into smaller cores. The formation of cores appears to be a three stage process: first, growth of the TI leads to rapid fragmentation of the slab; second, relatively small fragments acquire mass via gas-accretion and/or merger and third, sufficiently massive fragments become susceptible to the gravitational instability and sub-fragment to form smaller cores. We investigate typical properties of clumps (and smaller cores) resulting from this fragmentation process. Findings of this work support the suggestion that the weak velocity field usually observed in dense clumps and smaller cores is likely seeded by the growth of dynamic instabilities. Simulations were performed using the smooth particle hydrodynamics algorithm.

Shape and size directed self-selection in organic cage formation

The selective formation of a single isomer of a 3+2] self-assembled organic cage from a reaction mixture of an unsymmetrical aldehyde and a flexible amine is discussed. The experimental and theoretical findings suggest that in such a process, the geometric features of the aldehyde play a key role.

Preferential polarization and its reversal in polycrystalline BiFeO3/La0.5Sr0.5CoO3 heterostructures

Polycrystalline BiFeO3 thin films were grown on La0.5Sr0.5CoO3 buffered Pt (200)/TiO2/SiO2/Si substrates under different oxygen partial pressures (10, 25, 50 and 100 mTorr) by puked laser ablation. Piezo-response Force Microscopy and Piezo-Force Spectroscopy have shown that all the films are ferroelectric in nature with locally switchable domains. It has also revealed a preferential downward domain orientation in as-grown films grown under lower oxygen partial pressure (10 and 25 mTorr) with a reversal of preferential domain orientation as the oxygen partial pressure is increased to 100 mTorr during laser ablation. Such phenomena are atypical of multi-grained polycrystalline ferroelectric films and have been discussed On the basis of detect formation with changing growth conditions. For the 50 mTorr grown film, asymmetric domain stability and retention during write-read studies has been observed which is attributed to grain-size-related defect concentration, affecting pinning centres that inhibit domain wall motion. (C) 2015 Elsevier Ltd. All rights reserved.

Stability of Filaments in Star-Forming Clouds and the Formation of Prestellar Cores in Them

The exact process(es) that generate(s) dense filaments which then form prestellar cores within them is unclear. Here we study the formation of a dense filament using a relatively simple set-up of a pressure-confined, uniform-density cylinder. We examine if its propensity to form a dense filament and further, to the formation of prestellar cores along this filament, bears on the gravitational state of the initial volume of gas. We report a radial collapse leading to the formation of a dense filamentary cloud is likely when the initial volume of gas is at least critically stable (characterised by the approximate equality between the mass line-density for this volume and its maximum value). Though self-gravitating, this volume of gas, however, is not seen to be in free-fall. This post-collapse filament then fragments along its length due to the growth of a Jeans-like instability to form prestellar cores. We suggest dense filaments in typical star-forming clouds classified as gravitationally super-critical under the assumption of: (i) isothermality when in fact, they are not, and (ii) extended radial profiles as against pressure-truncated, that significantly over-estimates their mass line-density, are unlikely to experience gravitational free-fall. The radial density and temperature profile derived for this post-collapse filament is consistent with that deduced for typical filamentary clouds mapped in recent surveys of nearby star-forming regions.

One-pot synthesis of a TiO2-CdS nano-heterostructure assembly with enhanced photocatalytic activity

An unprecedented morphology of a titanium dioxide (TiO2) and cadmium sulfide (CdS) self-assembly obtained using a `truly' one-pot and highly cost effective method with a multi-gram scale yield is reported here. The TiO2-CdS assembly, comprising of TiO2 and CdS nanoparticles residing next to each other homogeneously self-assembling into `woollen knitting ball' like microspheres, exhibited remarkable potential as a visible light photocatalyst with high recyclability.

Extremely High Near Field Enhancement in a Novel Plasmonic Nano Material used for Photovoltage Generation

Enhancement of localized electric field near metal (plasmonic) nanostructures can have various interesting applications in sensing, imaging, photovoltage generation etc., for which significant efforts are aimed towards developing plasmonic systems with well designed and large electromagnetic response. In this paper, we discuss the wafer scale fabrication and optical characterization of a unique three dimensional plasmonic material. The near field enhancement in the visible range of the electromagnetic spectrum obtained in these structures (order of 106), is close to the fundamental limit that can be obtained in this and similar EM field enhancement schemes. The large near field enhancement has been reflected in a huge Raman signal of graphene layer in close proximity to the plasmonic system, which has been validated with FEM simulations. We have integrated graphene photodetectors with this material to obtain record photovoltage generation, with responsivity as high as A/W. As far as we know, this is the highest sensitivity obtained in any plasmonic-graphene hybrid photodetection system till date.

Phase formation and stability of alloy phases in free nanoparticles: some insights

This paper explores phase formation and phase stability in free nanoparticles of binary alloys. A procedure for estimating the size and composition dependent free energies incorporating the contributions from the interfaces has been presented. Both single phase solid solution and two phase morphology containing interphase interfaces have been considered. A free energy scenario has been evaluated for two binary alloy systems Ag-Ni and Ag-Cu to predict the microstructure of the alloy nanoparticles at different size ranges as a function of composition. Both Ag-Cu and Ag-Ni systems exhibit wide bulk immiscibility. Ag-Ni nanoparticles were synthesized using the wet chemical synthesis technique whereas Ag-Cu nanoparticles were synthesized using laser ablation of a Ag-Cu target immersed in distilled water. Microstructural and compositional characterization of Ag-Ni and Ag-Cu nanoparticles on a single nanoparticle level was conducted using transmission electron microscopy. Nanoparticle microstructures observed from the microscopic investigation have been correlated with thermodynamic calculation results. It is shown that the observed two phase microstructure consisting of Ag-Ni solid solution in partial decomposed state coexisting with pure Ag phases in the case of Ag-Ni nanoparticles can be only be rationalized by invoking the tendency for phase separation of an initial solid solution with increase in nanoparticle size. Smaller sized Ag-Ni nanoparticles prefer a single phase solid solution microstructure. Due to an increase in particle size during the synthesis process the initial solid solution decomposes into an ultrafine scale phase separated microstructure. We have shown that it is necessary to invoke critical point phenomenon and wetting transition in systems showing a critical point that leads to phase separated Ag-Ni nanoparticles providing a catalytic substrate for the nucleation of equilibrium Ag over it. In the case of the Ag-Cu system, we report the experimental observation of a core shell structure at small sizes. This can be rationalized in terms of a metastable solid solution. It is argued that the nucleation barrier can prevent the formation of biphasic morphology with an internal interface. In such a situation, demixing of the solid solution can bring the system to a lower energy configuration. This has lead to the observed core-shell morphology in the Ag-Cu system during room temperature synthesis.

Self-assembled ZnO nanoparticles on ZnO microsheet: ultrafast synthesis and tunable photoluminescence properties

We report on the tunable photoluminescence characteristics of porous ZnO microsheets fabricated within 1-5 min of microwave irradiation in the presence of a capping agent such as citric acid, and mixture of citric acid with polyvinylpyrrolidone (PVP). The UV emission intensity reduces to 60% and visible emission increases tenfold when the molar concentration of citric acid is doubled. Further diminution of the intensity of UV emission (25%) is observed when PVP is mixed with citric acid. The addition of nitrogen donor ligands to the parent precursor leads to a red shift in the visible luminescence. The deep level emission covers the entire visible spectrum and gives an impression of white light emission from these ZnO samples. The detailed luminescence mechanism of our ZnO samples is described with the help of a band diagram constructed by using the theoretical models that describe the formation energy of the defect energy levels within the energy band structure. Oxygen vacancies play the key role in the variation of the green luminescence in the ZnO microsheets. Our research findings provide an insight that it is possible to retain the microstructure and simultaneously introduce defects into ZnO. The growth of the ZnO microsheets may be due to the self assembly of the fine sheets formed during the initial stage of nucleation.

Do carboximide-carboxylic acid combinations form co-crystals? The role of hydroxyl substitution on the formation of co-crystals and eutectics

Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co- crystals or eutectics for the studied carboxylic acid/imide combinations.

Controlled material transport and multidimensional patterning at small length scales using electromigration

Electromigration, mostly known for its damaging effects in microelectronic devices, is basically a material transport phenomenon driven by the electric field and kinetically controlled by diffusion. In this work, we show how controlled electromigration can be used to create scientifically interesting and technologically useful micro-/nano-scale patterns, which are otherwise extremely difficult to fabricate using conventional cleanroom practices, and present a few examples of such patterns. In a solid thin-film structure, electromigration is used to generate pores at preset locations for enhancing the sensitivity of a MEMS sensor. In addition to electromigration in solids, the flow instability associated with the electromigration-induced long-range flow of liquid metals is shown to form numerous structures with high surface area to volume ratio. In very thin solid films on non-conductive substrates, solidification of flow-affected region results in the formation of several features, such as nano-/micro-sized discrete metallic beads, 3D structures consisting of nano-stepped stairs, etc.