Diverse functions of restriction-modification systems in addition to cellular defense

Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.

Microstructural and mechanical behavior study of suction cast Nb-Si binary alloys

The solidification pathways of Nb rich Nb-Si alloys when processed under non-equilibrium conditions require understanding. Continuing with our earlier work on alloying additions in single eutectic composition 1,2], we report a detailed characterization of the microstructures of Nb-Si binary alloys with wide composition range (10-25 at% Si). The alloys are processed using chilled copper mould suction casting. This has allowed us to correlate the evolution of microstructure and phases with different possible solidification pathways. Finally these are correlated with mechanical properties through studies on deformation using mechanical testing under indentation and compressive loads. It is shown that microstructure modification can significantly influence the plasticity of these alloys.

Stable and Potent Analogues Derived from the Modification of the Dicarbonyl Moiety of Curcumin

Curcumin has shown promising therapeutic utilities for many diseases, including cancer; however, its clinical application is severely limited because of its poor stability under physiological conditions. Here we find that curcumin also loses its activity instantaneously in a reducing environment. Curcumin can exist in solution as a tautomeric mixture of keto and enol forms, and the enol form was found to be responsible for the rapid degradation of the compound. To increase the stability of curcumin, several analogues were synthesized in which the diketone moiety of curcumin was replaced by isoxazole (compound 2) and pyrazole (compound 3) groups. Isoxazole and pyrazole curcumins were found to be extremely stable at physiological pH, in addition to reducing atmosphere, and they can kill cancer cells under serum-depleted condition. Using molecular modeling, we found that both compounds 2 and 3 could dock to the same site of tubulin as the parent molecule, curcumin. Interestingly, compounds 2 and 3 also show better free radical scavenging activity than curcumin. Altogether, these results strongly suggest that compounds 2 and 3 could be good replacements for curcumin in future drug development.

An enthalpy method for modeling eutectic solidification

This paper presents a new micro-scale model for solidification of eutectic alloys. The model is based on the enthalpy method and simulates the growth of adjacent alpha and beta phases from a melt of eutectic composition in a two-dimensional Eulerian framework. The evolution of the two phases is obtained from the solution of volume averaged energy and species transport equations which are formulated using the nodal enthalpy and concentration potential values. The three phases are tracked using the beta-phase fraction and the liquid fraction values in all the computational nodes. Solutal convection flow field in the domain is obtained from the solution of volume-averaged momentum and continuity equations. The governing equations are solved using a coupled explicit-implicit scheme. The model is qualitatively validated with Jackson-Hunt theory. Results show expected eutectic growth pattern and proper species transfer and diffusion field ahead of the interface. Capabilities of the model such as lamella width selection, division of lamella into thinner lamellae and the presence of solutal convection are successfully demonstrated. The present model can potentially be incorporated into the existing framework of enthalpy based micro-scale dendritic solidification models thus leading to an efficient generalized microstructure evolution model. (C) 2014 Elsevier Inc. All rights reserved.

Modification of Extended Open Frameworks with Fluorescent Tags for Sensing Explosives: Competition between Size Selectivity and Electron Deficiency

Three new electron-rich metal-organic frameworks (MOF-1-MOF-3) have been synthesized by employing ligands bearing aromatic tags. The key role of the chosen aromatic tags is to enhance the -electron density of the luminescent MOFs. Single-crystal X-ray structures have revealed that these MOFs form three-dimensional porous networks with the aromatic tags projecting inwardly into the pores. These highly luminescent electron-rich MOFs have been successfully utilized for the detection of explosive nitroaromatic compounds (NACs) on the basis of fluorescence quenching. Although all of the prepared MOFs can serve as sensors for NACs, MOF-1 and MOF-2 exhibit superior sensitivity towards 4-nitrotoluene (4-NT) and 2,4-dinitrotoluene (DNT) compared to 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrobenzene (TNB). MOF-3, on the other hand, shows an order of sensitivity in accordance with the electron deficiencies of the substrates. To understand such anomalous behavior, we have thoroughly analyzed both the steady-state and time-resolved fluorescence quenching associated with these interactions. Determination of static Stern-Volmer constants (K-S) as well as collisional constants (K-C) has revealed that MOF-1 and MOF-2 have higher K-S values with 4-NT than with TNT, whereas for MOF-3 the reverse order is observed. This apparently anomalous phenomenon was well corroborated by theoretical calculations. Moreover, recyclability and sensitivity studies have revealed that these MOFs can be reused several times and that their sensitivities towards TNT solution are at the parts per billion (ppb) level.

Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al2Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al2Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm. (C) 2014 Author(s).

Structural and magnetic properties of ultra-small scale eutectic CoFeZr alloys

Aiming to develop high mechanical strength and toughness by tuning ultrafine lamellar spacing of magnetic eutectic alloys, we report the mechanical and magnetic properties of the binary eutectic alloys Co90.5Zr9.5 and Fe90.2Zr9.8, as well as the pseudo-binary eutectic alloys Co82.4Fe8Zr9.6, Co78Fe12.4Zr9.6 and Co49.2Fe49.2Zr9.6 developed by suction-casting. The lower lamellar spacing around 100 nm of the eutectics Co49.2Fe49.2Zr9.6 yields a high hardness of 713(+/- 20) VHN. Magnetic measurements reveal high magnetic moment of 1.92 mu B (at 5 K) and 1.82 mu B (at 300 K) per formula unit for this composition. The magnetization vs. applied field data at 5 K show a directional preference to some extent and therefore smaller non-collinear magnetization behavior compared to Co11Zr2 reported in the literature due to exchange frustration and transverse spin freezing owing to the presence of smaller Zr content. The decay of magnetization as a function of temperature along the easy axis of magnetization of all the eutectic compositions can be described fairly well by the spin wave excitation equation Delta M/M(0) = BT3/2 + CT5/2. (C) 2014 Elsevier B.V. All rights reserved.

Development of alloys with high strength at elevated temperatures by tuning the bimodal microstructure in the Al-Cu-Ni eutectic system

The development of high-strength aluminum alloys that can operate at 250 degrees C and beyond remains a challenge to the materials community. In this paper we report preliminary development of nanostructural Al-Cu-Ni ternary alloys containing alpha-Al, binary Al2Cu and ternary Al2Cu4Ni intermetallics. The alloys exhibits fracture strength of similar to 1 GPa with similar to 9% fracture strain at room temperature. At 300 degrees C, the alloy retains the high strength. The reasons for such significant mechanical properties are rationalized by unraveling the roles and response of various microstructural features. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Surface modification of textured silicon and its wetting behaviour

Textured silicon (Si) substrate were prepared using various texturing methods both chemical and physical and their water contact angle, surface topography and Raman spectra were studied and investigated. The effect of plasma and chemical treatment on micro/nanostructure and roughness of the surface with and without deposition of Octadecyltrichlorosilane (ODTS, Cl3Si (CH3)(17)), self-assembled monolayer (SAM) is investigated for achieving higher water contact angle (theta(c)). The importance of synergism of texturing with deposition of ODTS SAM in preparing superhydrophobic silicon surfaces has been discussed. It is shown that superhydrophobic silicon surfaces can be achieved on silicon surfaces by coating with ODTS, irrespective of whether it is textured or not, polished or unpolished, provided a chemical treatment is given to the surface prior to the ODTS coating.

Modification of crosslinked chitosan membrane using NaY zeolite for pervaporation separation of water-isopropanol mixtures

The blocked diisocyanate crosslinked chitosan membrane was modified by incorporating different mass% of NaY zeolite. The physico-chemical properties of resulting composite membranes were studied using Fourier transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (WAXD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). The mechanical properties of the membranes were studied using universal testing machine (UTM). After measuring the equilibrium swelling, membranes were subjected to pervaporation for separation of water-isopropanol mixtures. Both flux and selectivity were increased with increasing NaY zeolite content in the membranes. The membrane containing 40 mass% of NaY zeolite exhibited the highest separation selectivity of 11,241 with a flux of 11.37 x 10(-2) kg/m(2) h for 10 mass% of water in the feed. The total flux and flux of water are almost overlapping each other, suggesting that these membranes could be effectively used to break the azeotropic point of water-isopropanol mixture. From the temperature dependent diffusion and permeation values, the Arrhenius activation parameters were estimated. All the composite membranes exhibited lower activation energy compared to crosslinked membrane, indicating that the permeants require less energy during the process because of molecular sieving action attributed to the presence of sodalite and super cages in the framework of Nay zeolite. The Henry's mode of sorption dominates the process, giving an endothermic contribution. (C) 2014 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.

A CONVENIENT MODIFICATION OF THE FISCHER INDOLE SYNTHESIS WITH A SOLID ACID

A new one-pot version of the titled reaction involves heating a mixture of a carbonyl compound, a phenylhydrazine, and the cation exchange resin Amberlite IR 120 in refluxing ethanol. A variety of enolizable aldehydes, and ketones and several substituted phenylhydrazines could thus be converted to the corresponding indoles in excellent yields (70-88%). Reaction times were typically 6-10 h, with the resin being then filtered off and the product isolated after minimal workup.

Intermetallic eutectic alloys in the Ni-Al-Zr system with attractive high temperature properties

We describe a group of alloys with ultrahigh strength of about 2 GPa at 700 degrees C and exceptional oxidation resistance to 1100 degrees C. These alloys exploit intermetallic phases with stable oxide forming elements that combine to form fine nanometric scale structures through eutectic transformations in ternary systems. The alloys offer engineering tensile plasticity of about 4% at room temperature though both conventional dislocation mechanisms and twinning in the more complex intermetallic constituent, along with slip lengths that are restricted by the interphase boundaries in the eutectics.

Enhancing the mechanical and biological performance of a metallic biomaterial for orthopedic applications through changes in the surface oxide layer by nanocrystalline surface modification

Nanostructured metals are a promising class of biomaterials for application in orthopedics to improve the mechanical performance and biological response for increasing the life of biomedical implants. Surface mechanical attrition treatment (SMAT) is an efficient way of engineering nanocrystalline surfaces on metal substrates. In this work, 316L stainless steel (SS), a widely used orthopedic biomaterial, was subjected to SMAT to generate a nanocrystalline surface. Surface nanocrystallization modified the nature of the oxide layer present on the surface. It increased the corrosion-fatigue strength in saline by 50%. This increase in strength is attributed to a thicker oxide layer, residual compressive stresses, high strength of the surface layer, and lower propensity for intergranular corrosion in the nanocrystalline layer. Nanocrystallization also enhanced osteoblast attachment and proliferation. Intriguingly, wettability and surface roughness, the key parameters widely acknowledged for controlling the cellular response remained unchanged after nanocrystallization. The observed cellular behavior is explained in terms of the changes in electronic properties of the semiconducting passive oxide film present on the surface of 316L SS. Nanocrystallization increased the charge carrier density of the n-type oxide film likely preventing denaturation of the adsorbed cell-adhesive proteins such as fibronectin. In addition, a net positive charge developed on the otherwise neutral oxide layer, which is known to facilitate cellular adhesion. The role of changes in the electronic properties of the oxide films on metal substrates is thus highlighted in this work. This study demonstrates the advantages of nanocrystalline surface modification by SMAT for processing metallic biomaterials used in orthopedic implants.