Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

TeV scale implications of non commutative space time in laboratory frame with polarized beams

We analyze e(+)e(-) -> gamma gamma, e(-)gamma -> e(-)gamma and gamma gamma -> e(+)e(-) processes within the Seiberg-Witten expanded noncommutative scenario using polarized beams. With unpolarized beams the leading order effects of non commutativity starts from second order in non commutative(NC) parameter i.e. O(Theta(2)), while with polarized beams these corrections appear at first order (O(Theta')) in cross section. The corrections in Compton case can probe the magnetic component(Theta(B)) while in Pair production and Pair annihilation probe the electric component((Theta) over right arrow (E)) of NC parameter. We include the effects of earth rotation in our analysis. This study is done by investigating the effects of non commutativity on different time averaged cross section observables. The results which also depends on the position of the collider, can provide clear and distinct signatures of the model testable at the International Linear Collider(ILC).

An Empirical Analysis of Heterogeneity in IEEE 802.11 MAC Protocol Implementations and its Implications

Wireless LAN (WLAN) market consists of IEEE 802.11 MAC standard conformant devices (e.g., access points (APs), client adapters) from multiple vendors. Certain third party certifications such as those specified by the Wi-Fi alliance have been widely used by vendors to ensure basic conformance to the 802.11 standard, thus leading to the expectation that the available devices exhibit identical MAC level behavior. In this paper, however, we present what we believe to be the first ever set of experimental results that highlight the fact that WLAN devices from different vendors in the market can have heterogeneous MAC level behavior. Specifically, we demonstrate with examples and data that in certain cases, devices may not be conformant with the 802.11 standard while in other cases, they may differ in significant details that are not a part of mandatory specifications of the standard. We argue that heterogeneous MAC implementations can adversely impact WLAN operations leading to unfair bandwidth allocation, potential break-down of related MAC functionality and difficulties in provisioning the capacity of a WLAN. However, on the positive side, MAC level heterogeneity can be useful in applications such as vendor/model level device fingerprinting.

Biofuel production and implications for land use, food production and environment in India

There is a large interest in biofuels in India as a substitute to petroleum-based fuels, with a purpose of enhancing energy security and promoting rural development. India has announced an ambitious target of substituting 20% of fossil fuel consumption by biodiesel and bioethanol by 2017. India has announced a national biofuel policy and launched a large program to promote biofuel production, particularly on wastelands: its implications need to be studied intensively considering the fact that India is a large developing country with high population density and large rural population depending upon land for their livelihood. Another factor is that Indian economy is experiencing high growth rate, which may lead to enhanced demand for food, livestock products, timber, paper, etc., with implications for land use. Studies have shown that area under agriculture and forest has nearly stabilized over the past 2-3 decades. This paper presents an assessment of the implications of projected large-scale biofuel production on land available for food production, water, biodiversity, rural development and GHG emissions. The assessment will be largely focused on first generation biofuel crops, since the Indian program is currently dominated by these crops. Technological and policy options required for promoting sustainable biofuel production will be discussed. (C) 2010 Elsevier Ltd. All rights reserved.

Time-dependent transitions with time-space noncommutativity and its implications in quantum optics

We study the time-dependent transitions of a quantum-forced harmonic oscillator in noncommutative R(1,1) perturbatively to linear order in the noncommutativity theta. We show that the Poisson distribution gets modified, and that the vacuum state evolves into a `squeezed' state rather than a coherent state. The time evolutions of uncertainties in position and momentum in vacuum are also studied and imply interesting consequences for modeling nonlinear phenomena in quantum optics.

Implications of unitarity and analyticity for the D pi form factors

We consider the vector and scalar form factors of the charm-changing current responsible for the semileptonic decay D -> pi/nu. Using as input dispersion relations and unitarity for the moments of suitable heavy-light correlators evaluated with Operator Product Expansions, including O(alpha(2)(s)) terms in perturbative QCD, we constrain the shape parameters of the form factors and find exclusion regions for zeros on the real axis and in the complex plane. For the scalar form factor, a low-energy theorem and phase information on the unitarity cut are also implemented to further constrain the shape parameters. We finally propose new analytic expressions for the D pi form factors, derive constraints on the relevant coefficients from unitarity and analyticity, and briefly discuss the usefulness of the new parametrizations for describing semileptonic data.

Electrochemical oxidation of boron containing compounds on titanium carbide and its implications to direct fuel cells

Electrochemical oxidation of sodium borohydride (NaBH(4)) and ammonia borane (NH(3)BH(3)) (AB) have been studied on titanium carbide electrode. The oxidation is followed by using cyclic voltammetry, chronoamperometry and polarization measurements. A fuel cell with TiC as anode and 40 wt% Pt/C as cathode is constructed and the polarization behaviour is studied with NaBH(4) as anodic fuel and hydrogen peroxide as catholyte. A maximum power density of 65 mW cm(-2) at a load current density of 83 mA cm(-2) is obtained at 343 K in the case of borhydride-based fuel cell and a value of 85 mW cm(-2) at 105 mA cm(-2) is obtained in the case of AB-based fuel cell at 353 K. (C) 2011 Elsevier Ltd. All rights reserved.

Charge transfer complex states in diketopyrrolopyrrole polymers and fullerene blends: Implications for organic solar cell efficiency

The spectral photocurrent characteristics of two donor-acceptor diketopyrrolopyrrole (DPP)-based copolymers (PDPP-BBT and TDPP-BBT) blended with a fullerene derivative [6,6]-phenyl C-61-butyric acid methyl ester (PCBM) were studied using Fourier-transform photocurrent spectroscopy (FTPS) and monochromatic photocurrent (PC) method. PDPP-BBT: PCBM shows the onset of the lowest charge transfer complex (CTC) state at 1.42 eV, whereas TDPP-BBT: PCBM shows no evidence of the formation of a midgap CTC state. The FTPS and PC spectra of P3HT:PCBM are also compared. The larger singlet state energy difference of TDPP-BBT and PCBM compared to PDPP-BBT/P3HT and PCBM obliterates the formation of a midgap CTC state resulting in an enhanced photovoltaic efficiency over PDPP-BBT: PCBM. (C) 2011 American Institute of Physics. [doi:10.1063/1.3670043]

Patent intelligence and its implications for patent productivity

The prevailing hypercompetitive environment has made it essential for organizations to gather competitive intelligence from environmental scanning. The knowledge gained leads to organizational learning, which stimulates increased patent productivity. This paper highlights five practices that aid in developing patenting intelligence and empirically verifies to what extent this organizational learning leads to knowledge gains and financial gains realized from consequent higher patent productivity. The model is validated based on the perceptions of professionals with patenting experience from two of the most aggressively patenting sectors in today’s economy, viz., IT and pharmaceutical sectors (n=119). The key finding of our study suggests that although organizational learning from environmental scanning exists, the application of this knowledge for increasing patent productivity lacks due appreciation. This missing link in strategic analysis and strategy implementation has serious implications for managers which are briefly discussed in this paper.

Distinct Roles of FANCO/RAD51C Protein in DNA Damage Signaling and Repair Implications for Fanconi Anemia and Breast Cancer Susceptibility

RAD51C, a RAD51 paralog, has been implicated in homologous recombination (HR), and germ line mutations in RAD51C are known to cause Fanconi anemia (FA)-like disorder and breast and ovarian cancers. The role of RAD51C in the FA pathway of DNA interstrand cross-link (ICL) repair and as a tumor suppressor is obscure. Here, we report that RAD51C deficiency leads to ICL sensitivity, chromatid-type errors, and G(2)/M accumulation, which are hallmarks of the FA phenotype. We find that RAD51C is dispensable for ICL unhooking and FANCD2 monoubiquitination but is essential for HR, confirming the downstream role of RAD51C in ICL repair. Furthermore, we demonstrate that RAD51C plays a vital role in the HR-mediated repair of DNA lesions associated with replication. Finally, we show that RAD51C participates in ICL and double strand break-induced DNA damage signaling and controls intra-S-phase checkpoint through CHK2 activation. Our analyses with pathological mutants of RAD51C that were identified in FA and breast and ovarian cancers reveal that RAD51C regulates HR and DNA damage signaling distinctly. Together, these results unravel the critical role of RAD51C in the FA pathway of ICL repair and as a tumor suppressor.

NMR Structure Implications of Enhanced Efficacy of Obestatin Fragment Analogs

Obestatin is a more recently discovered hormone that is encoded by the ghrelin gene and produced in the stomach and gut. We report NMR analysis on synthetic Obestatin (OB23), a 23 residue peptide, along with three overlapping fragments of the same in methanol solvent as a first step towards structure activity relationship. Selective substitutions on the promising N-terminal and middle fragments of obestatin have been carried out in order to improve the efficacy and potency. In the N-terminal fragment two peptides were obtained by the replacement of Gly (8) with a-aminoisobutyric acid (Aib, U) and Phe (F5) with Cyclohexylalanine (Cha). In case of the middle fragment both Gly (3) and Gly (8) were replaced with Aib residues. The rationale being, these unusual amino acids could provide protection from immediate degradation and aid structure stabilization. Our previous studies showed that the N-terminal and the middle fragment were unstructured and hence this substitution would directly evaluate the effect of structure on the activity of these fragment analogs. Detailed NMR analysis clearly demonstrates formation of helical secondary structure in all the peptide analogues and provides justification for relative activities reported by our group previously (Nagaraj et al. 2009).