Sequence effects in structures of the dinucleotides d-pApT AND d-pTpA

The H1',H2' and H2″ regions of the 270-MHz PMR spectra of two deoxydinucleotides, d-pTpA and d-pApT, have been analyzed. The coupling constants in the sugar ring indicate that both A and T sugars have a tendency to acquire 2E conformations. There is also a marginal difference in the 2E populations of the T sugar in the two dinucleotides. The trends in the chemical shifts of base protons indicate different stacking of the bases in d-pApT and d-pTpA. The sequence effects on base stacking and pentose conformation are discussed.

Nature of the thiamin-binding protein from chicken egg yolk

A simple, rapid and efficient procedure for the purification of thiamin-binding protein from chicken egg yolk was developed. The method involved removal, by exclusion, of lipoproteins from DEAE-cellulose and subsequent elution of water-soluble proteins held on the ion-exchanger with 1 M-NaCl, followed by treatment of the eluted protein fraction with an aqueous suspension of dextran/charcoal to generate apoprotein from the holoprotein. The resultant protein fraction was subjected to bioaffinity chromatography on thiamin pyrophosphate--AE (aminoethyl)-Sepharose. The protein eluted specifically with 10 microM-thiamin at pH 7.0, was homogeneous by the criteria of polyacrylamide-gel disc electrophoresis, had a mol.wt. of 38 000 +/- 2000 and was not a glycoprotein. The purified thiamin-binding protein specifically interacted with riboflavin-binding protein with no detectable deleterious affect on its (14C)thiamin-binding capacity. The protein bound [14C]thiamin with a molar ratio of 1.0, with dissociation constant (Kd) 0.41 microM. This protein-ligand interaction was inhibited by thiamin analogues and antagonists. The absorption spectrum of the protein in the presence of thiamin exhibited significant hypochromism at the 278 nm band, indicating the involvement of aromatic amino acid residues of the protein, during its binding to the ligand. The protein cross-reacted with the monospecific antiserum to egg-white thiamin-binding protein, showing thereby that thiamin-binding proteins present in chicken egg yolk and white are the products of the same structural gene.

Plasma polymer and biomolecule modification of 3-D scaffolds for tissue engineering

Plasma polymerization was used to coat a melt electrospun polycaprolactone scaffold to improve cell attachment and organization. Plasma polymerization was performed using an amine containing monomer, allylamine, which then allowed for the subsequent immobilization of biomolecules i.e. heparin and fibroblast growth factor-2. The stability of the plasma polymerized amine-coating was demonstrated by X-ray photoelectron spectroscopy analysis and imaging time-of-flight secondary ion mass spectrometry revealed that a uniform plasma amine-coating was deposited throughout the scaffold. Based upon comparison with controls it was evident that the combination scaffold aided cell ingress and the formation of distinct fibroblast and keratinocyte layers.

Optical and magnetic resonance studies of the interaction of metallo tetraphenylporphyrins with nitrobenzofuroxan

Metallo tetraphenylporphyrins form I : I molecular complexes with 4,6-dinitrobenzofuroxan. The molecular association is described in terms of T-n. interaction with porphyrins functioning as donors. The association constants and thermodynamic parameters have been evaluated using optical absorption and 'H nmr spectral methods. Based on the binding constants, the donor ability of various metalloporphyrins can be arranged in the following order: Pd(I1) > Co(I1) > Cu(I1) > Ni(I1) - VO(1V) - 2H > Zn(l1). Electron paramagnetic resonance studies of the complexes reveal that the IT-complexation results in changes in the electronic structure of the central metal ions which are reflected in the changes in the M-N 5 bonding. The dipolar contribution to the acceptor proton chemical shifts in the CoTPP complex has been partitioned from ring current contributions using the shifts observed in the ZnTPP complex. The shifts, along with the line broadening ratios observed for the CoTPP complex, are used to arrive at the possible solution structures of the complexes.

Microbial L-phenylalanine ammonia-lyase. Purification, subunit structure and kinetic properties of the enzyme from Rhizoctonia solani

Phenylalanine ammonia-lyase (EC 4.3.1.5) was purified to homogeneity from the acetone-dried powders of the mycelial felts of the plant pathogenic fungus Rhizoctonia solani. 2. A useful modification in protamine sulphate treatment to get substantial purification of the enzyme in a single-step is described. 3. The purified enzyme shows bisubstrate activity towards L-phenylalanine and L-tyrosine. 4. It is sensitive to carbonyl reagents and the inhibition is not reversed by gel filtration. 5. The molecular weight of the enzyme as determined by Sephadex G-200 chromatography and sucrose-density-gradient centrifugation is around 330000. 6. The enzyme is made up of two pairs of unidentical subunits, with a molecular weight of 70000 (alpha) and 90000 (beta) respectively. 7. Studies on initial velocity versus substrate concentration have shown significant deviations from Michaelis-Menten kinetics. 8. The double-reciprocal plots are biphasic (concave downwards) and Hofstee plots show a curvilinear pattern. 9. The apparent Km value increases from 0.18 mM to as high as 5.0 mM with the increase in the concentration of the substrate and during this process the Vmax, increases by 2-2.5-fold. 10. The value of Hill coefficient is 0.5. 11. Steady-state rates of phenylalanine ammonia-lyase reaction in the presence of inhibitors like D-phenylalanine, cinnamic, p-coumaric, caffeic, dihydrocaffeic and phenylpyruvic acid have shown that only one molecule of each type of inhibitor binds to a molecule of the enzyme. These observations suggest the involvement of negative homotropic interactions in phenylalanine ammonia-lyase. 12. The enzyme could not be desensitized by treatment with HgCl2, p-chloromercuribenzoic acid or by repeated freezing and thawing.

The logic of data-sense: Thinking through Learning Personalisation

Big Data and Learning Analytics’ promise to revolutionise educational institutions, endeavours, and actions through more and better data is now compelling. Multiple, and continually updating, data sets produce a new sense of ‘personalised learning’. A crucial attribute of the datafication, and subsequent profiling, of learner behaviour and engagement is the continual modification of the learning environment to induce greater levels of investment on the parts of each learner. The assumption is that more and better data, gathered faster and fed into ever-updating algorithms, provide more complete tools to understand, and therefore improve, learning experiences through adaptive personalisation. The argument in this paper is that Learning Personalisation names a new logistics of investment as the common ‘sense’ of the school, in which disciplinary education is ‘both disappearing and giving way to frightful continual training, to continual monitoring'.

Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-d-glucuronidase (heparanase)

Mammalian heparanase is an endo-β-glucuronidase associated with cell invasion in cancer metastasis, angiogenesis and inflammation. Heparanase cleaves heparan sulfate proteoglycans in the extracellular matrix and basement membrane, releasing heparin/heparan sulfate oligosaccharides of appreciable size. This in turn causes the release of growth factors, which accelerate tumor growth and metastasis. Heparanase has two glycosaminoglycan-binding domains; however, no three-dimensional structure information is available for human heparanase that can provide insights into how the two domains interact to degrade heparin fragments. We have constructed a new homology model of heparanase that takes into account the most recent structural and bioinformatics data available. Heparin analogs and glycosaminoglycan mimetics were computationally docked into the active site with energetically stable ring conformations and their interaction energies were compared. The resulting docked structures were used to propose a model for substrates and conformer selectivity based on the dimensions of the active site. The docking of substrates and inhibitors indicates the existence of a large binding site extending at least two saccharide units beyond the cleavage site (toward the nonreducing end) and at least three saccharides toward the reducing end (toward heparin-binding site 2). The docking of substrates suggests that heparanase recognizes the N-sulfated and O-sulfated glucosamines at subsite +1 and glucuronic acid at the cleavage site, whereas in the absence of 6-O-sulfation in glucosamine, glucuronic acid is docked at subsite +2. These findings will help us to focus on the rational design of heparanase-inhibiting molecules for anticancer drug development by targeting the two heparin/heparan sulfate recognition domains.

The influence of esterification of carboxyl groups of ribonuclease-a on its structure and immunological activity

The effect of modification of carboxyl groups of Ribonuclease-Aa on the enzymatic activity and the antigenic structure of the protein has been studied. Modification of four of the eleven free carboxyl groups of the protein by esterification in anhydrous methanol/0.1 M hydrochloric acid resulted in nearly 80% loss in enzymatic activity but had very little influence on the antigenic structure of the protein. Further increases in the modification of the carboxyl groups caused a progressive loss in immunological activity, and the fully methylated RNase-A exhibited nearly 30% immunological activity. Concomitant with this change in the antigenic structure of the protein, the ability of the molecule to complement with RNase-S-protein increased, clearly indicating the unfolding of the peptide "tail" from the remainder of the molecule. The susceptibility to proteolysis, accessibility of methionine residues for orthobenzoquinone reaction and the loss in immunological activity of the more extensively esterified derivatives of RNase-A are suggestive of the more flexible conformation of these derivatives as compared with the compact native conformation. The fact that even the fully methylated RNase-A retains nearly 30% of its immunological activity suggested that the modified protein contained antibody recognizable residual native structure, which presumably accommodates some antigenic determinants.

Titration calorimetric studies to elucidate the specificity of the interactions of polymyxin B with lipopolysaccharides and lipid A

Lipopolysaccharide (LPS), the major cell wall constituent of Gram-negative bacteria, evokes a multitude of biological effects in mammals including pyrogenicity and toxic shock syndrome. Polymyxin B (PmB), a polycationic cyclic peptide, is known to neutralize most of its activities. The nature of the interaction of PmB with LPS and lipid A was investigated by isothermal titration calorimetry. PmB binds to LPS as well as lipid A stoichiometrically and non-co-operatively with micromolar affinity. These interactions are driven primarily by a favourable change in entropy (delta S) and are endothermic in nature. These positive changes in enthalpies decrease with increasing temperature, yielding a heat capacity change, delta Cp, of -2385 J.mol-1.degree-1 for PmB-LPS interactions while the binding of PmB to lipid A displays a delta Cp of -2259 J.mol-1.degree-1. The negative heat capacity changes provide strong evidence for the role of hydrophobic interactions as the driving force for the association of PmB with LPS and lipid A. A correlation of the energetics of these interactions with analyses of the molecular models of PmB suggests that a cluster of solvent-exposed non-polar amino acid side-chains that line one surface of the molecule, together with a ring of positively charged residues on its other surface, are responsible for its strong and stoichiometric binding to LPS.

The evolution of loop structures in flux rings within the solar convection zone

Choudhuri and Gilman (1987) considered certain implications of the hypothesis that the magnetic flux within the Sun is generated at the bottom of the convection zone and then rises through it. Taking flux rings symmetric around the rotation axis and using reasonable values of different parameters, they found that the Coriolis force deflects these flux rings into trajectories parallel to the rotation axis so that they emerge at rather high latitudes. This paper looks into the question of whether the action of the Coriolis force is subdued when the initial configuration of the flux ring has non-axisymmetries in the form of loop structures. The results depend dramatically on whether the flux ring with the loops lies completely within the convection zone or whether the lower parts of it are embedded in the stable layers underneath the convection zone. In the first case, the Coriolis force supresses the non-axisymmetric perturbations so that the flux ring tends to remain symmetric and the trajectories are very similar to those of Choudhuri and Gilman (1987). In the second case, however, the lower parts of the flux ring may remain anchored underneath the bottom of the convection zone, but the upper parts of the loops still tend to move parallel to the rotation axis and emerge at high latitudes. Thus the problem of the magnetic flux not being able to come out at the sunspot latitudes still persists after the non-axisymmetries in the flux rings are taken into account.

Enantiospecific synthesis of ABC-ring system of A-nor and abeo 4(3 -> 2) tetra and pentacyclic triterpenes

Enantiospecific synthesis of ABC-ring systems of A-nor and abeo 4(3 -> 2) tetra and pentacyclic triterpenes has been accomplished starting from the readily available monoterpene (R)-carvone. (R)-Carvone was used as the B-ring of the target molecules. A lithium-liquid ammonia mediated cyclisation of delta,epsilon-unsaturated ester was employed for the cyclopentannulation at the C-5 and C-6 carbons of carvone and an RCM reaction was employed for the cyclohexannulation to generate the ABC-ring system of A-nor tetra and pentacyclic triterpenes. The strategy has been extended for the synthesis of the ABC-ring system of abeo 4(3 -> 2) tetra and pentacyclic triterpenes. (C) 2009 Elsevier Ltd. All rights reserved.

Dual-frequency characteristics of Minkowski-square ring antennas

Fractal Minkowski curves to design a compact dual-frequency microstrip ring antenna are proposed. Sides of a square ring have been selectively replaced with first and second iterations of the generalised fractal geometry to design a smaller antenna with dual-frequency operation. This behaviour has been explained based on current distributions on the antenna structure. Measured results compare well with electromagnetic simulations.

Growth and Modification of Cluster-Assembled Thin Films

Thin film applications have become increasingly important in our search for multifunctional and economically viable technological solutions of the future. Thin film coatings can be used for a multitude of purposes, ranging from a basic enhancement of aesthetic attributes to the addition of a complex surface functionality. Anything from electronic or optical properties, to an increased catalytic or biological activity, can be added or enhanced by the deposition of a thin film, with a thickness of only a few atomic layers at the best, on an already existing surface. Thin films offer both a means of saving in materials and the possibility for improving properties without a critical enlargement of devices. Nanocluster deposition is a promising new method for the growth of structured thin films. Nanoclusters are small aggregates of atoms or molecules, ranging in sizes from only a few nanometers up to several hundreds of nanometers in diameter. Due to their large surface to volume ratio, and the confinement of atoms and electrons in all three dimensions, nanoclusters exhibit a wide variety of exotic properties that differ notably from those of both single atoms and bulk materials. Nanoclusters are a completely new type of building block for thin film deposition. As preformed entities, clusters provide a new means of tailoring the properties of thin films before their growth, simply by changing the size or composition of the clusters that are to be deposited. Contrary to contemporary methods of thin film growth, which mainly rely on the deposition of single atoms, cluster deposition also allows for a more precise assembly of thin films, as the configuration of single atoms with respect to each other is already predetermined in clusters. Nanocluster deposition offers a possibility for the coating of virtually any material with a nanostructured thin film, and therein the enhancement of already existing physical or chemical properties, or the addition of some exciting new feature. A clearer understanding of cluster-surface interactions, and the growth of thin films by cluster deposition, must, however, be achieved, if clusters are to be successfully used in thin film technologies. Using a combination of experimental techniques and molecular dynamics simulations, both the deposition of nanoclusters, and the growth and modification of cluster-assembled thin films, are studied in this thesis. Emphasis is laid on an understanding of the interaction between metal clusters and surfaces, and therein the behaviour of these clusters during deposition and thin film growth. The behaviour of single metal clusters, as they impact on clean metal surfaces, is analysed in detail, from which it is shown that there exists a cluster size and deposition energy dependent limit, below which epitaxial alignment occurs. If larger clusters are deposited at low energies, or cluster-surface interactions are weaker, non-epitaxial deposition will take place, resulting in the formation of nanocrystalline structures. The effect of cluster size and deposition energy on the morphology of cluster-assembled thin films is also determined, from which it is shown that nanocrystalline cluster-assembled films will be porous. Modification of these thin films, with the purpose of enhancing their mechanical properties and durability, without destroying their nanostructure, is presented. Irradiation with heavy ions is introduced as a feasible method for increasing the density, and therein the mechanical stability, of cluster-assembled thin films, without critically destroying their nanocrystalline properties. The results of this thesis demonstrate that nanocluster deposition is a suitable technique for the growth of nanostructured thin films. The interactions between nanoclusters and their supporting surfaces must, however, be carefully considered, if a controlled growth of cluster-assembled thin films, with precisely tailored properties, is to be achieved.

Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.

The generalized anomeric effect in the 1,3-thiazolidines: Evidence forboth sulphur and nitrogen as electron donors. Crystal structures of various N-acylthiazolidines including mercury(II) complexes. Possible relevance to penicillin action

Evidence for the generalized anomeric effect (GAE) in the N-acyl-1,3-thiazolidines, an important structural motif in the penicillins, was sought in the crystal structures of N-(4-nitrobenzoyl)-1,3-thiazolidine and its (2:1) complex with mercuric chloride, N-acetyl-2-phenyl-1,3-thiazolidine, and the (2:1) complex of N-benzoyl-1,3-thiazolidine with mercuric bromide. An inverse relationship was generally observed between the. C-2-N and C-2-S bond lengths of the thiazolidine ring, supporting the existence of the GAE. (Maximal bond length changes were similar to 0.04 angstrom for C-2-N-3, S-1-C-2, and similar to 0.08 angstrom for N-3-C-6.) Comparison with N-acylpyrrolidines and tetrahydrothiophenes indicates that both the nitrogen-to-sulphur and sulphur-to-nitrogen GAE's operate simultaneously in the 1,3-thiazolidines, the former being dominant. (This is analogous to the normal and exo-anomeric effects in pyranoses, and also leads to an interesting application of Baldwin's rules.) The nitrogen-to-sulphur GAE is generally enhanced in the mercury(II) complexes (presumably via coordination at the sulphur); a 'competition' between the GAE and the amide resonance of the N-acyl moiety is apparent. There is evidence for a 'push-pull' charge transfer between the thiazolidine moieties in the mercury(II) complexes, and for a 'back-donation' of charge from the bromine atoms to the thiazolidine moieties in the HgBr2 complex. (The sulphur atom appears to be sp(2) hybridised in the mercury(II) complexes, possibly for stereoelectronic reasons.) These results are apparently relevant to the mode of action of the penicillins. (c) 2006 Elsevier B.V. All rights reserved.