Engineering the properties of D-amino acid oxidases by a rational and a directed evolution approach

D-amino acid oxidase (DAAO) is a FAD-containing flavoprotein that dehydrogenates the D-isomer of amino acids to the corresponding imino acids, coupled with the reduction of FAD. The cofactor then reoxidizes on molecular oxygen and the imino acid hydrolyzes spontaneously to the alpha-keto acid and ammonia. In vitro DAAO displays broad substrate specificity, acting on several neutral and basic D-amino acids: the most efficient substrates are amino acids with hydrophobic side chains. D-aspartic acid and D-glutamic acid are not substrates for DAAO. Through the years, it has been the subject of a number of structural, functional and kinetic investigations. The most recent advances are represented by site-directed mutagenesis studies and resolution of the 3D-structure of the enzymes from pig, human and yeast. The two approaches have given us a deeper understanding of the structure-function relationships and promoted a number of investigations aimed at the modulating the protein properties. By a rational and/or a directed evolution approach, DAAO variants with altered substrate specificity (e.g., active on acidic or on all D-amino acids), increased stability (e.g., stable up to 60 degrees C), modified interaction with the flavin cofactor, and altered oligomeric state were produced. The aim of this paper is to provide an overview of the most recent research on the engineering of DAAOs to illustrate their new intriguing properties, which also have enabled us to pursue new biotechnological applications.     

Poly (N-isopropylacrylamide) microgel-based assemblies

Thermally responsive poly (N-isopropylacrylamide) (pNIPAm)-based hydrogel particles (microgels) have been extensively studied over past few decades. We, and others, have found that assemblies of these microgels exhibit unique properties that make them useful such as nonfouling surface coatings, drug release/delivery vehicles, and sensors. In this submission, we review our efforts to develop novel water remediation systems and optical devices from pNIPAm-based microgels. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3004–3020     

Hydrogen‐Bonding Induced Alternate Stacking of Donor (D) and Acceptor (A) Chromophores and their Supramolecular Switching to Segregated States

This paper reports comprehensive studies on the mixed assembly of bis‐(trialkoxybenzamide)‐functionalized dialkoxynaphthalene (DAN) donors and naphthalene‐diimide (NDI) acceptors due the cooperative effects of hydrogen bonding, charge‐transfer (CT) interactions, and solvophobic effects. A series of DAN as well as NDI building blocks have been examined (wherein the relative distance between the two amide groups in a particular chromophore is the variable structural parameter) to understand the structure‐dependent variation in mode of supramolecular assembly and morphology (organogel, reverse vesicle, etc.) of the self‐assembled material. Interestingly, it was observed that when the amide functionalities are introduced to enhance the self‐assembly propensity, the mode of co‐assembly among the DAN and NDI chromophores no longer remained trivial and was dictated by a relatively stronger hydrogen‐bonding interaction instead of a weak CT interaction. Consequently, in a highly non‐polar solvent like methylcyclohexane (MCH), although kinetically controlled CT‐gelation was initially noticed, within a few hours the system sacrificed the CT‐interaction and switched over to the more stable self‐sorted gel to maximize the gain in enthalpy from the hydrogen‐bonding interaction. In contrast, in a relatively less non‐polar solvent such as tetrachloroethylene (TCE), in which the strength of hydrogen bonding is inherently weak, the contribution of the CT interaction also had to be accounted for along with hydrogen bonding leading to a stable CT‐state in the gel or solution phase. The stability and morphology of the CT complex and rate of supramolecular switching (from CT to segregated state) were found to be greatly influenced by subtle structural variation of the building blocks, solvent polarity, and the DAN/NDI ratio. For example, in a given D–A pair, by introducing just one methylene unit in the spacer segment of either of the building blocks a complete change in the mode of co‐assembly (CT state or segregated state) and the morphology (1D fiber to 2D reverse vesicle) was observed. The role of solvent polarity, structural variation, and D/A ratio on the nature of co‐assembly, morphology, and the unprecedented supramolecular‐switching phenomenon have been studied by detail spectroscopic and microscopic experiments in a gel as well as in the solution state and are well supported by DFT calculations.     

Hydrogen‐Bonding‐Mediated Vesicular Assembly of Functionalized Naphthalene–Diimide‐Based Bolaamphiphile and Guest‐Induced Gelation in Water

This paper describes the spontaneous vesicular assembly of a naphthalene–diimide (NDI)‐based non‐ionic bolaamphiphile in aqueous medium by using the synergistic effects of π‐stacking and hydrogen bonding. Site isolation of the hydrogen‐bonding functionality (hydrazide), a strategy that has been adopted so elegantly in nature, has been executed in this system to protect these moieties from the bulk water so that the distinct role of hydrogen bonding in the self‐assembly of hydrazide‐functionalized NDI building blocks could be realized, even in aqueous solution. Furthermore, the electron‐deficient NDI‐based bolaamphiphile could engage in donor–acceptor (D–A) charge‐transfer (CT) interactions with a water‐insoluble electron‐rich pyrene donor by virtue of intercalation of the latter chromophore in between two NDI building blocks. Remarkably, even when pyrene was located between two NDI blocks, intermolecular hydrogen‐bonding networks between the NDI‐linked hydrazide groups could be retained. However, time‐dependent AFM studies revealed that the radius of curvature of the alternately stacked D–A assembly increased significantly, thereby leading to intervesicular fusion, which eventually resulted in rupturing of the membrane to form 1D fibers. Such 2D‐to‐1D morphological transition produced CT‐mediated hydrogels at relatively higher concentrations. Instead of pyrene, when a water‐soluble carboxylate‐functionalized pyrene derivative was used as the intercalator, non‐covalent tunable in‐situ surface‐functionalization could be achieved, as evidenced by the zeta‐potential measurements.     

Hydrogen-bonding-mediated vesicular assembly of functionalized naphthalene-diimide-based bolaamphiphile and guest-induced gelation in water

This paper describes the spontaneous vesicular assembly of a naphthalene-diimide (NDI)-based non-ionic bolaamphiphile in aqueous medium by using the synergistic effects of π-stacking and hydrogen bonding. Site isolation of the hydrogen-bonding functionality (hydrazide), a strategy that has been adopted so elegantly in nature, has been executed in this system to protect these moieties from the bulk water so that the distinct role of hydrogen bonding in the self-assembly of hydrazide-functionalized NDI building blocks could be realized, even in aqueous solution. Furthermore, the electron-deficient NDI-based bolaamphiphile could engage in donor-acceptor (D-A) charge-transfer (CT) interactions with a water-insoluble electron-rich pyrene donor by virtue of intercalation of the latter chromophore in between two NDI building blocks. Remarkably, even when pyrene was located between two NDI blocks, intermolecular hydrogen-bonding networks between the NDI-linked hydrazide groups could be retained. However, time-dependent AFM studies revealed that the radius of curvature of the alternately stacked D-A assembly increased significantly, thereby leading to intervesicular fusion, which eventually resulted in rupturing of the membrane to form 1D fibers. Such 2D-to-1D morphological transition produced CT-mediated hydrogels at relatively higher concentrations. Instead of pyrene, when a water-soluble carboxylate-functionalized pyrene derivative was used as the intercalator, non-covalent tunable in-situ surface-functionalization could be achieved, as evidenced by the zeta-potential measurements.     

Elemental analysis in bed sediment samples of Karnafuli estuarine zone in the Bay of Bengal by instrumental neutron activation analysis

The concentration of rare earths and other elements have been determined in the bed sediment samples of Karnafuli estuarine zone in the Bay of Bengal by instrumental neutron activation analysis (INAA). The samples and the standards soil-5, soil-7, coal fly ash and pond sediment were prepared and simultaneously irradiated for short and long time at the TRIGA Mark-II research reactor facility of Atomic Energy Research Establishment, Savar, Dhaka. The maximum themal neutron flux was of the order of 10¹³ n·cm^–2·s^–1. After irradiation the radioactivity of the product nuclides was measured by using a high resolution high purity germanium detector system. Analysis of -ray spectra and quantitative analysis of the elemental concentration were done via the software GANAAS, it has been possible to determine the concentration level of 27 elements including the rare earths La, Ce, Sm, Eu, Tb, Dy and Yb and uranium and thorium.     

Estimation of the Sea Level Muon Spectra at Different Zenith Angles below 10 TeV Energy

The moderate energy primary cosmic ray nucleon spectrum has been calculated from the direct measurements of Webber et al., Seo et al., and Menn et al. along with the other results surveyed by Swordy. Using these directly measured primary mass composition results all particle primary nucleon energy spectrum has been constructed using superposition model to estimate the energy spectra of muons from the decay of the cosmic ray non-prompt and prompt mesons in the atmosphere. The Z-factors have been estimated from the CERN LEBC-EHS on the Lorentz invariant cross section results on pp ^±X and pp K^±X inclusive reactions and FNAL data on ^±p ^±X reactions, and duly corrected for A--A collisions. Using these Z-factors the meson energy spectra in the atmosphere have been calculated. The sea level muon energy spectra at zenith angles 0°, 45°, 72°, and 75° have been derived from the decay of non-prompt mesons by adopting standard diffusion equation of hadronic cascades. The contribution of charmed mesons to muon spectrum has also been accounted by adapting the conventional procedure. The derived differential sea level muon energy spectra for energies 10 TeV have been found to follow the power law fits of the form N (E) const. E ^-. Our estimated muon energy spectra at zenith angles 75° have been found comparable with the global spectrograph muon flux results of MARS, DEIS, and MSU groups.     

Energy of unitary Cayley graphs and gcd-graphs

This work is based on ideas of Ili? [A. Ili?, The energy of unitary Cayley graphs, Linear Algebra Appl. 431 (2009) 1881-1889] on the energy of unitary Cayley graph. For a finite commutative ring R with unity , the unitary Cayley graph of R is the Cayley graph whose vertex set is R and the edge set is {{a,b}:a,b∈Randa-b∈R^×}, where R^× is the group of units of R. We study the eigenvalues of the unitary Cayley graph of a finite commutative ring and some gcd-graphs and compute their energy. Moreover, we obtain the energy for the complement of unitary Cayley graphs.     

Pressure drop of slug flow in microchannels with increasing void fraction: experiment and modeling

Pressure drop in a gas-liquid slug flow through a long microchannel of rectangular cross-section was investigated. Pressure measurements in a lengthy (～0.8 m) microchannel determined the pressure gradient to be constant in a flow where gas bubbles progressively expanded and the flow velocity increased due to a significant pressure drop. Most of the earlier studies of slug flow in microchannels considered systems where the expansion of the gas bubbles was negligible in the channel. In contrast, we investigated systems where the volume of the gas phase increased significantly due to a large pressure drop (up to 1811 kPa) along the channel. This expansion of the gas phase led to a significant increase in the void fraction, causing considerable flow acceleration. The pressure drop in the microchannel was studied for three gas-liquid systems; water-nitrogen, dodecane-nitrogen, and pentadecane-nitrogen. Inside the microchannel, local pressure was measured using a series of embedded membranes acting as pressure sensors. Our investigation of the pressure drop showed a linear trend over a wide range of void fractions and flow conditions in the two-phase flow. The lengths and the velocities of the liquid slugs and the gas bubbles were also studied along the microchannel by employing a video imaging technique. Furthermore, a model describing the gas-liquid slug flow in a long microchannel was developed to calculate the pressure drop under conditions similar to the experiments. An excellent agreement between the developed model and the experimental data was obtained.     

Chiral induction by helical neighbour: spectroscopic visualization of macroscopic-interaction among self-sorted donor and acceptor π-stacks

Supramolecular induction of chirality to a π-stacked dialkoxynaphthalene (DAN)-fiber (made of achiral building blocks) from a neighbouring helical naphthalenediimide (NDI)-fiber is reported. CD-studies helped in understanding the nature of co-assembly in the donor-acceptor chromophore mixture from molecular to macroscopic scale.