Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

Moment-Matched Lognormal Modeling of Uplink Interference with Power Control and Cell Selection

We develop an alternate characterization of the statistical distribution of the inter-cell interference power observed in the uplink of CDMA systems. We show that the lognormal distribution better matches the cumulative distribution and complementary cumulative distribution functions of the uplink interference than the conventionally assumed Gaussian distribution and variants based on it. This is in spite of the fact that many users together contribute to uplink interference, with the number of users and their locations both being random. Our observations hold even in the presence of power control and cell selection, which have hitherto been used to justify the Gaussian distribution approximation. The parameters of the lognormal are obtained by matching moments, for which detailed analytical expressions that incorporate wireless propagation, cellular layout, power control, and cell selection parameters are developed. The moment-matched lognormal model, while not perfect, is an order of magnitude better in modeling the interference power distribution.

Multi-hop Cooperative Wireless Networks: Diversity Multiplexing Tradeoff and Optimal Code Design

We consider single-source single-sink (ss-ss) multi-hop relay networks, with slow-fading links and single-antenna half-duplex relay nodes. While two-hop cooperative relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this paper, we identify two families of networks that are multi-hop generalizations of the two-hop network: K-Parallel-Path (KPP)networks and layered networks.KPP networks, can be viewed as the union of K node-disjoint parallel relaying paths, each of length greater than one. KPP networks are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the DMT of these families of networks completely for K > 3. Layered networks are networks comprising of layers of relays with edges existing only between adjacent layers, with more than one relay in each layer. We prove that a linear DMT between the maximum diversity dmax and the maximum multiplexing gain of 1 is achievable for single-antenna fully-connected layered networks. This is shown to be equal to the optimal DMT if the number of relaying layers is less than 4.For multiple-antenna KPP and layered networks, we provide an achievable DMT, which is significantly better than known lower bounds for half duplex networks.For arbitrary multi-terminal wireless networks with multiple source-sink pairs, the maximum achievable diversity is shown to be equal to the min-cut between the corresponding source and the sink, irrespective of whether the network has half-duplex or full-duplex relays. For arbitrary ss-ss single-antenna directed acyclic networks with full-duplex relays, we prove that a linear tradeoff between maximum diversity and maximum multiplexing gain is achievable.Along the way, we derive the optimal DMT of a generalized parallel channel and derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. We also give alternative and often simpler proofs of several existing results and show that codes achieving full diversity on a MIMO Rayleigh fading channel achieve full diversity on arbitrary fading channels. All protocols in this paper are explicit and use only amplify-and-forward (AF) relaying. We also construct codes with short block-lengths based on cyclic division algebras that achieve the optimal DMT for all the proposed schemes.Two key implications of the results in the paper are that the half-duplex constraint does not entail any rate loss for a large class of cooperative networks and that simple AF protocols are often sufficient to attain the optimal DMT

Structure of tandem and its implication for bifunctional intercalation into dna

Quinoxaline antibiotics (Fig. 1a, b) form a useful group of compounds for the study of drug–nucleic acid interactions1,2. They consist of a cross-bridged cyclic octadepsipeptide, variously modified, bearing two quinoxaline chromophores. These antibiotics intercalate bifunctionally into DNA2,3 probably via the narrow groove, forming a complex in which, most probably, two base pairs are sandwiched between the chromophores4,5. Depending on the nature of their sulphur-containing cross-bridge and modifications to their amino acid side chains, they display characteristic patterns of nucleotide sequence selectivity when binding to DNAs of different base composition and to synthetic polydeoxynucleotides4,6,7. This specificity has been tentatively ascribed to specific hydrogen-bonding interactions between functional groups in the DNA and complementary moieties on the peptide ring2,4,5. Variations in selectivity have been attributed both to changes in the conformation of the peptide backbone6 and no modifications of the cross-bridge7. These suggestions were made, however, in the absence of firm knowledge about the three-dimensional structure and conformation of the antibiotic molecules. We now report the X-ray structure analysis of the synthetic analogue of the antibiotic triostin A, TANDEM (des-N-tetramethyl triostin A) (Fig. 1c), which binds preferentially to alternating adenine-thymine sequences7. The X-ray structure provides a starting point for exploring the origin of this specificity and suggests possible models for the binding of other members of the quinoxaline series.

Coupled phonons, magnetic excitations, and ferroelectricity in AlFeO3: Raman and first-principles studies

We determine the nature of coupled phonons and magnetic excitations in AlFeO3 using inelastic light scattering from 5 to 315 K covering a spectral range from 100 to 2200 cm(-1) and complementary first-principles density functional theory-based calculations. A strong spin-phonon coupling and magnetic ordering-induced phonon renormalization are evident in (1) anomalous temperature dependence of many modes with frequencies below 850 cm(-1), particularly near the magnetic transition temperature T-c approximate to 250 K, and (2) distinct changes in band positions of high-frequency Raman bands between 1100 and 1800 cm(-1); in particular, a broad mode near 1250 cm(-1) appears only below T-c, attributed to the two-magnon Raman scattering. We also observe weak anomalies in the mode frequencies similar to 100 K due to a magnetically driven ferroelectric phase transition. Understanding of these experimental observations has been possible on the basis of first-principles calculations of the phonons' spectrum and their coupling with spins.

Patterned growth and differentiation of neural cells on polymer derived carbon substrates with micro/nano structures in vitro

The growth of neuroblastoma (N2a) and Schwann cells has been explored on polymer derived carbon substrates of varying micro and nanoscale geometries: resorcinol-formaldehyde (RE) gel derived carbon films and electrospun nanofibrous (similar to 200 nm diameter) mat and SU-8 (a negative photoresist) derived carbon micro-patterns. MTT assay and complementary lactate dehydrogenase (LDH) assay established cytocompatibility of RE derived carbon films and fibers over a period of 6 days in culture. The role of length scale of surface patterns in eliciting lineage-specific adaptive response along, across and on the interspacing between adjacent micropatterns (i.e., ``on'', ``across'' and ``off'') has been assayed. Textural features were found to affect 3',5'-cyclic AMP sodium salt-induced neurite outgrowth, over a wide range of length scales: from similar to 200 nm (carbon fibers) to similar to 60 mu m (carbon patterns). Despite their innate randomness, carbon nanofibers promoted preferential differentiation of N2a cells into neuronal lineage, similar to ordered micro-patterns. Our results, for the first time, conclusively demonstrate the potential of RE-gel and SU-8 derived carbon substrates as nerve tissue engineering platforms for guided proliferation and differentiation of neural cells in vitro. (C) 2013 Elsevier Ltd. All rights reserved.

Hot deformation behaviour and microstructure control in AlCrCuNiFeCo high entropy alloy

An AlCrCuNiFeCo high entropy alloy (HEA), which has simple face centered cubic (FCC) and body centered cubic (BCC) solid solution phases as the microstructural constituents, was processed and its high temperature deformation behaviour was examined as a function of temperature (700-1030 degrees C) and strain rate (10(-3)-10(-1) s(-1)), so as to identify the optimum thermo-mechanical processing (TMP) conditions for hot working of this alloy. For this purpose, power dissipation efficiency and deformation instability maps utilizing that the dynamic materials model pioneered by Prasad and co-workers have been generated and examined. Various deformation mechanisms, which operate in different temperature-strain rate regimes, were identified with the aid of the maps and complementary microstructural analysis of the deformed specimens. Results indicate two distinct deformation domains within the range of experimental conditions examined, with the combination of 1000 degrees C/10(-3) s(-1) and 1030 degrees C/10(-2) s(-1) being the optimum for hot working. Flow instabilities associated with adiabatic shear banding, or localized plastic flow, and or cracking were found for 700-730 degrees C/10(-3)-10(-1) s(-1) and 750-860 degrees C/10(-1.4)-10(-1) s(-1) combinations. A constitutive equation that describes the flow stress of AlCrCuNiFeCo alloy as a function of strain rate and deformation temperature was also determined. (C) 2014 Elsevier Ltd. All rights reserved.

Epithelial atrophy in oral submucous fibrosis is mediated by copper (II) and arecoline of areca nut

Exposure of oral cavity to areca nut is associated with several pathological conditions including oral submucous fibrosis (OSF). Histopathologically OSF is characterized by epithelial atrophy, chronic inflammation, juxtaepithelial hyalinization, leading to fibrosis of submucosal tissue and affects 0.5% of the population in the Indian subcontinent. As the molecular mechanisms leading to atrophied epithelium and fibrosis are poorly understood, we studied areca nut actions on human keratinocyte and gingival fibroblast cells. Areca nut water extract (ANW) was cytotoxic to epithelial cells and had a pro-proliferative effect on fibroblasts. This opposite effect of ANW on epithelial and fibroblast cells was intriguing but reflects the OSF histopathology such as epithelial atrophy and proliferation of fibroblasts. We demonstrate that the pro-proliferative effects of ANW on fibroblasts are dependent on insulin-like growth factor signalling while the cytotoxic effects on keratinocytes are dependent on the generation of reactive oxygen species. Treatment of keratinocytes with arecoline which is a component of ANW along with copper resulted in enhanced cytotoxicity which becomes comparable to IC50 of ANW. Furthermore, studies using cyclic voltammetry, mass spectrometry and plasmid cleavage assay suggested that the presence of arecoline increases oxidation reduction potential of copper leading to enhanced cleavage of DNA which could generate an apoptotic response. Terminal deoxynucleotidyl transferase dUTP Nick End Labeling assay and Ki-67 index of OSF tissue sections suggested epithelial apoptosis, which could be responsible for the atrophy of OSF epithelium.

Necessary and sufficient conditions for optimality in constrained general sum stochastic games

In this paper we first derive a necessary and sufficient condition for a stationary strategy to be the Nash equilibrium of discounted constrained stochastic game under certain assumptions. In this process we also develop a nonlinear (non-convex) optimization problem for a discounted constrained stochastic game. We use the linear best response functions of every player and complementary slackness theorem for linear programs to derive both the optimization problem and the equivalent condition. We then extend this result to average reward constrained stochastic games. Finally, we present a heuristic algorithm motivated by our necessary and sufficient conditions for a discounted cost constrained stochastic game. We numerically observe the convergence of this algorithm to Nash equilibrium. (C) 2015 Elsevier B.V. All rights reserved.

Electrically driven intracellular and extracellular nanomanipulators evoke neurogenic/cardiomyogenic differentiation in human mesenchymal stem cells

Nanomechanical intervention through electroactuation is an effective strategy to guide stem cell differentiation for tissue engineering and regenerative medicine. In the present study, we elucidate that physical forces exerted by electroactuated gold nanoparticles (GNPs) have a strong influence in regulating the lineage commitment of human mesenchymal stem cells (hMSCs). A novel platform that combines intracellular and extracellular GNPs as nano-manipulators was designed to trigger neurogenic/cardiomyogenic differentiation in hMSCs, in electric field stimulated culture condition. In order to mimic the native microenvironment of nerve and cardiac tissues, hMSCs were treated with physiologically relevant direct current electric field (DC EF) or pulsed electric field (PEF) stimuli, respectively. When exposed to regular intermittent cycles of DC EF stimuli, majority of the GNP actuated hMSCs acquired longer filopodial extensions with multiple branch-points possessing neural-like architecture. Such morphological changes were consistent with higher mRNA expression level for neural-specific markers. On the other hand, PEF elicited cardiomyogenic differentiation, which is commensurate with the tubelike morphological alterations along with the upregulation of cardiac specific markers. The observed effect was significantly promoted even by intracellular actuation and was found to be substrate independent. Further, we have substantiated the participation of oxidative signaling, G0/G1 cell cycle arrest and intracellular calcium Ca2+] elevation as the key upstream regulators dictating GNP assisted hMSC differentiation. Thus, by adopting dual stimulation protocols, we could successfully divert the DC EF exposed cells to differentiate predominantly into neural-like cells and PEF treated cells into cardiomyogenic-like cells, via nanoactuation of GNPs. Such a novel multifaceted approach can be exploited to combat tissue loss following brain injury or heart failure. (C) 2015 Elsevier Ltd. All rights reserved.