Gene expression in osteoblast cells treated with submicron to nanometer hydroxyapatite-mullite eluate particles

The present research focused on determining the effect of hydroxyapatite-20 wt% mullite (H20M) particle eluates on apoptosis and differentiation of human fetal osteoblast (hFOB) cells. The H20M particles (257 +/- 37 nm) were prepared, starting with the production of a nanocomposite using a unique route of spark plasma sintering, followed by a repeated grinding-cryo treatment and elution process. Tetrazolium based cytotoxicity assay results showed a time-and dose-dependent effect of H20M particle eluates on hFOB cytotoxicity. In particular, the results revealed statistically reduced cell viability after hFOB were exposed to the above 10% H20M (257 +/- 37 nm) eluates for 48 h. The apoptotic cell death triggered by H20M treatment was proven by the analysis of molecular markers of apoptosis, that is, the Bcl-2 family of genes. hFOB expression of Bcl-xL and Bcl-xS significantly increased 25.6- and 25.2-fold for 50% of H20M concentrations, respectively. The ratio of Bcl-xL/Bax (4.01) decreased 2-fold for hFOB exposed to 100% of H20M eluates than that for 10% H20M eluate (7.94) treated hFOB cells. On the other hand, the Bcl-xS/Bax ratio for the 10% H20M eluate was 4.15-fold, whereas for 100% H20M eluates, it was 11.55-fold. Specifically, the anti-apoptotic effect of the H20M particle eluates was corroborated by the up-regulation of bone cell differentiation marker genes such as, collagen type I, cbfa, and osteocalcin. In summary, the present work clearly demonstrated that H20M submicron to nanometer composite particle eluates have a minimal effect on hFOB apoptosis and can even up-regulate the expression of bone cell markers at the molecular level.

Direct Band-to-Band Tunneling in Reverse Biased MoS2 Nanoribbon p-n Junctions

We investigate the direct band-to-band tunneling (BTBT) in a reverse biased molybdenum disulfide (MoS2) nanoribbon p-n junction by analyzing the complex band structure obtained from semiempirical extended Huckel method under relaxed and strained conditions. It is demonstrated that the direct BTBT is improbable in relaxed monolayer nanoribbon; however, with the application of certain uniaxial tensile strain, the material becomes favorable for it. On the other hand, the relaxed bilayer nanoribbon is suitable for direct BTBT but becomes unfavorable when the applied uniaxial tensile or compressive strain goes beyond a certain limit. Considering the Wentzel-Kramers-Brillouin approximation, we evaluate the tunneling probability to estimate the tunneling current for a small applied reverse bias. Reasonably high tunneling current in the MoS2 nanoribbons shows that it can take advantage over graphene nanoribbon in future tunnel field-effect transistor applications.

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): Importance of steric and electronic effects on the unusual cyclization of the sulfenic acid intermediate to a sulfenyl amide

The redox regulation of protein tyrosine phosphatase 1B (PTP1B) via the unusual transformation of its sulfenic acid (PTP1B-SOH) to a cyclic sulfenyl amide intermediate is studied by using small molecule chemical models. These studies suggest that the sulfenic acids derived from the H2O2-mediated reactions o-amido thiophenols do not efficiently cyclize to sulfenyl amides and the sulfenic acids produced in situ can be trapped by using methyl iodide. Theoretical calculations suggest that the most stable conformer of such sulfenic acids are stabilized by n(O) -> sigma* (S-OH) orbital interactions, which force the -OH group to adopt a position trans to the S center dot center dot center dot O interaction, leading to an almost linear arrangement of the O center dot center dot center dot S-O moiety and this may be the reason for the slow cyclization of such sulfenic acids to their corresponding sulfenyl amides. On the other hand, additional substituents at the 6-position of o-amido phenylsulfenic acids that can induce steric environment and alter the electronic properties around the sulfenic acid moiety by S center dot center dot center dot N or S center dot center dot center dot O nonbonded interactions destabilize the sulfenic acids by inducing strain in the molecule. This may lead to efficient the cyclization of such sulfenic acids. This model study suggests that the amino acid residues in the close proximity of the sulfenic acid moiety in PTP1B may play an important role in the cyclization of PTP1B-SOH to produce the corresponding sulfenyl amide.

Electrostatic modulation of periodic potentials in a two-dimensional electron gas: from antidot lattice to quantum dot lattice

We use a dual gated device structure to introduce a gate-tuneable periodic potential in a GaAs/AlGaAs two dimensional electron gas (2DEG). Using only a suitable choice of gate voltages we can controllably alter the potential landscape of the bare 2DEG, inducing either a periodic array of antidots or quantum dots. Antidots are artificial scattering centers, and therefore allow for a study of electron dynamics. In particular, we show that the thermovoltage of an antidot lattice is particularly sensitive to the relative positions of the Fermi level and the antidot potential. A quantum dot lattice, on the other hand, provides the opportunity to study correlated electron physics. We find that its current-voltage characteristics display a voltage threshold, as well as a power law scaling, indicative of collective Coulomb blockade in a disordered background.

Effect of strain on electronic and thermoelectric properties of few layers to bulk MoS2

The sensitive dependence of the electronic and thermoelectric properties of MoS2 on applied strain opens up a variety of applications in the emerging area of straintronics. Using first-principles-based density functional theory calculations, we show that the band gap of a few layers of MoS2 can be tuned by applying normal compressive (NC) strain, biaxial compressive (BC) strain, and biaxial tensile (BT) strain. A reversible semiconductor-to-metal transition (S-M transition) is observed under all three types of strain. In the case of NC strain, the threshold strain at which the S-M transition occurs increases when the number of layers increase and becomes maximum for the bulk. On the other hand, the threshold strain for the S-M transition in both BC and BT strains decreases when the number of layers increase. The difference in the mechanisms for the S-M transition is explained for different types of applied strain. Furthermore, the effect of both strain type and the number of layers on the transport properties are also studied using Botzmann transport theory. We optimize the transport properties as a function of the number of layers and the applied strain. 3L- and 2L-MoS2 emerge as the most efficient thermoelectric materials under NC and BT strain, respectively. The calculated thermopower is large and comparable to some of the best thermoelectric materials. A comparison among the feasibility of these three types of strain is also discussed.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Implication of a sigma-Methane Complex en Route to Elimination of Methane from a Ruthenium Complex: An Experimental and Theoretical Investigation

The five-coordinated 16-electron complex Ru(Me)(dppe)(2)]OTf] (3) undergoes methane elimination at room temperature to afford the ortho-metalated species (dppe){(C6H5)(C6H4)PCH2CH2P(C6H5)(2)}Ru]OTf] (7). Methane elimination, monitored using NMR spectroscopy, revealed no intermediate throughout the reaction. The NOE between Ru-Me protons and ortho phenyl protons and an agostic interaction trans to the methyl group were found in complex 3 by NMR spectroscopy, which form the basis for three plausible pathways for methane elimination and ortho metalation: pathway I (through spatial interaction), pathway II (through oxidative addition and reductive elimination), and pathway III (through agostic interaction). Methane elimination from complex 3 via pathway I was discounted, since it involves interactions through space and not through bonds. Moreover, the calculated energy barrier for the pathway I transition state was quite high (71.3 kcal/mol), which also indicates that this pathway is very unlikely. Furthermore, no spectroscopic evidence for oxidatively added seven-coordinated Ru(IV) species was found and the computed energy barrier of the transition state for pathway II was moderately high (41.1 kcal/mol), which suggests that this cannot be the right pathway for methane elimination and ortho-metalation of complex 3. On the other hand, indirect evidence in the form of chemical reactions point to the most plausible pathway for methane elimination, pathway III, via the intermediacy of a sigma-CH4 complex that could not be found spectroscopically. DFT calculations at several levels on this pathway showed an initial low-barrier rearrangement through TS1 to a square-pyramidal intermediate wherein methyl and agostic C-H are cis to each other. Migration of hydrogen from agostic C-H and elimination of methane proceed through the transition state TS2, which retains a weak metal-H bonding through most parts of the reaction coordinate. Upon comparison of all three pathways, pathway III was found to be the most likely for methane elimination and ortho-metalation of complex 3.

Interferon-Gamma and Nitric Oxide Synthase 2 Mediate the Aggregation of Resident Adherent Peritoneal Exudate Cells: Implications for the Host Response to Pathogens

Interferon-gamma (Ifn gamma), a key macrophage activating cytokine, plays pleiotropic roles in host immunity. In this study, the ability of Ifn gamma to induce the aggregation of resident mouse adherent peritoneal exudate cells (APECs), consisting primarily of macrophages, was investigated. Cell-cell interactions involve adhesion molecules and, upon addition of Ifn gamma, CD11b re-localizes preferentially to the sites of interaction on APECs. A functional role of CD11b in enhancing aggregation is demonstrated using Reopro, a blocking reagent, and siRNA to Cd11b. Studies with NG-methyl-L-arginine (LNMA), an inhibitor of Nitric oxide synthase (Nos), NO donors, e.g., S-nitroso-N-acetyl-DL-penicillamine (SNAP) or Diethylenetriamine/ nitric oxide adduct (DETA/NO), and Nos2(-/-) mice identified Nitric oxide (NO) induced by Ifn gamma as a key regulator of aggregation of APECs. Further studies with Nos2(-/-) APECs revealed that some Ifn. responses are independent of NO: induction of MHC class II and CD80. On the other hand, Nos2 derived NO is important for other functions: motility, phagocytosis, morphology and aggregation. Studies with cytoskeleton depolymerizing agents revealed that Ifn gamma and NO mediate the cortical stabilization of Actin and Tubulin which contribute to aggregation of APECs. The biological relevance of aggregation of APECs was delineated using infection experiments with Salmonella Typhimurium (S. Typhimurium). APECs from orally infected, but not uninfected, mice produce high amounts of NO and aggregate upon ex vivo culture in a Nos2-dependent manner. Importantly, aggregated APECs induced by Ifn gamma contain fewer intracellular S. Typhimurium compared to their single counterparts post infection. Further experiments with LNMA or Reopro revealed that both NO and CD11b are important for aggregation; in addition, NO is bactericidal. Overall, this study elucidates novel roles for Ifn gamma and Nos2 in regulating Actin, Tubulin, CD11b, motility and morphology during the aggregation response of APECs. The implications of aggregation or ``group behavior'' of APECs are discussed in the context of host resistance to infectious organisms.

ANRC Hybrid Test Bed Implementation and an End-to-End Performance Characterization of Dynamic Spectrum Access

An abundance of spectrum access and sensing algorithms are available in the dynamic spectrum access (DSA) and cognitive radio (CR) literature. Often, however, the functionality and performance of such algorithms are validated against theoretical calculations using only simulations. Both the theoretical calculations and simulations come with their attendant sets of assumptions. For instance, designers of dynamic spectrum access algorithms often take spectrum sensing and rendezvous mechanisms between transmitter-receiver pairs for granted. Test bed designers, on the other hand, either customize so much of their design that it becomes difficult to replicate using commercial off the shelf (COTS) components or restrict themselves to simulation, emulation /hardware-in-Ioop (HIL), or pure hardware but not all three. Implementation studies on test beds sophisticated enough to combine the three aforementioned aspects, but at the same time can also be put together using COTS hardware and software packages are rare. In this paper we describe i) the implementation of a hybrid test bed using a previously proposed hardware agnostic system architecture ii) the implementation of DSA on this test bed, and iii) the realistic hardware and software-constrained performance of DSA. Snapshot energy detector (ED) and Cumulative Summation (CUSUM), a sequential change detection algorithm, are available for spectrum sensing and a two-way handshake mechanism in a dedicated control channel facilitates transmitter-receiver rendezvous.

Interplay of electrostatics and lipid packing determines the binding of charged polymer coated nanoparticles to model membranes

Understanding of nanoparticle-membrane interactions is useful for various applications of nanoparticles like drug delivery and imaging. Here we report on the studies of interaction between hydrophilic charged polymer coated semiconductor quantum dot nanoparticles with model lipid membranes. Atomic force microscopy and X-ray reflectivity measurements suggest that cationic nanoparticles bind and penetrate bilayers of zwitterionic lipids. Penetration and binding depend on the extent of lipid packing and result in the disruption of the lipid bilayer accompanied by enhanced lipid diffusion. On the other hand, anionic nanoparticles show minimal membrane binding although, curiously, their interaction leads to reduction in lipid diffusivity. It is suggested that the enhanced binding of cationic QDs at higher lipid packing can be understood in terms of the effective surface potential of the bilayers which is tunable through membrane lipid packing. Our results bring forth the subtle interplay of membrane lipid packing and electrostatics which determine nanoparticle binding and penetration of model membranes with further implications for real cell membranes.

Fracture Testing at Small-Length Scales: From Plasticity in Si to Brittleness in Pt

The field of micro-/nano-mechanics of materials has been driven, on the one hand by the development of ever smaller structures in devices, and, on the other, by the need to map property variations in large systems that are microstructurally graded. Observations of `smaller is stronger' have also brought in questions of accompanying fracture property changes in the materials. In the wake of scattered articles on micro-scale fracture testing of various material classes, this review attempts to provide a holistic picture of the current state of the art. In the process, various reliable micro-scale geometries are shown, challenges with respect to instrumentation to probe ever smaller length scales are discussed and examples from recent literature are put together to exhibit the expanse of unusual fracture response of materials, from ductility in Si to brittleness in Pt. Outstanding issues related to fracture mechanics of small structures are critically examined for plausible solutions.

Reply to Discussion on ``Bearing capacity of circular footings over rock mass by using axisymmetric quasi lower bound finite element limit analysis'' Comput. Geotech. 70 (2015) 138-149]

A discussion has been provided for the comments raised by the discusser (Clausen, 2015)1] on the article recently published by the authors (Chakraborty and Kumar, 2015). The effect of exponent alpha for values of GSI approximately smaller than 30 becomes more critical. On the other hand, for greater values of GSI, the results obtained by the authors earlier remain primarily independent of alpha and can be easily used. (C) 2015 Elsevier Ltd. All rights reserved.