Conformations of the amino terminal tetrapeptide of emerimicins and antiamoebin in solution and in the solid state

The conformations of Boc-l-Phe-(AiB)3-OH (1) and Boc-l-Phe-(Aib)3-OMe (2) which correspond to the amino terminal sequence of the emerimicins and antiamoebins have been studied in solution using 270 MHz 1H n.m.r. In dimethyl sulphoxide solution both peptides show the presence of two strongly solvent shielded Aib NH groups, consistent with a consecutive β-turn conformation, involving the Aib(3) and Aib(4) NH groups in intramolecular 4 → I hydrogen bonds. This folded conformation is maintained for 2 in chloroform solution. Nuclear Overhauser effect studies provide evidence for a Type II Phe-Aib β-turn. An X-ray diffraction study of Boc-(d,l)-Phe-(Aib)3-OH establishes a single type III(III′) β-turn conformation with Aib(2)-Aib(3) as the corner residues. A single intramolecular 4 → I hydrogen bond between Phe(I) CO and Aib(4) NH groups is observed in the crystal. The solution conformation may incorporate a consecutive type II-III′ structure for the Phe(1)-Aib(2)-Aib(3) segment, with the initial type II β-turn being destabilized by intermolecular interactions in the solid state.

Effect of amino acid substitutions at the subunit interface on the stabiity and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the dimer interface of thymidylate synthase

The significance of two interface arginine residues on the structural integrity of an obligatory dimeric enzyme thymidylate synthase (TS) from Lactobacillus casei was investigated by thermal and chemical denaturation. While the R178F mutant showed apparent stability to thermal denaturation by its decreased tendency to aggregate, the Tm of the R218K mutant was lowered by 5 degrees C. Equilibrium denaturation studies in guanidinium chloride (GdmCl) and urea indicate that in both the mutants, replacement of Arg residues results in more labile quaternary and tertiary interactions. Circular dichroism studies in aqueous buffer suggest that the protein interior in R218K may be less well-packed as compared to the wild type protein. The results emphasize that quaternary interactions may influence the stability of the tertiary fold of TS. The amino acid replacements also lead to notable alteration in the ability of the unfolding intermediate of TS to aggregate. The aggregated state of partially unfolded intermediate in the R178F mutant is stable over a narrower range of denaturant concentrations. In contrast, there is an exaggerated tendency on the part of R218K to aggregate in intermediate concentrations of the denaturant. The 3 A crystal structure of the R178F mutant reveals no major structural change as a consequence of amino acid substitution. The results may be rationalized in terms of mutational effects on both the folded and unfolded state of the protein. Site specific amino acid substitutions are useful in identifying specific regions of TS involved in association of non-native protein structures.

Jahn-Teller effect induced phase transitions in CsCuCl3

Occurence of the three Jahn-Teller effect induced phase transitions of CsCuCl3 at 423, 510 and 535 K has been established and the nature of the transitions examined by X-ray crystallography, far infrared spectroscopy and other techniques.

Lower Gastrointestinal Microbiota in Health and Irritable Bowel Syndrome : Characterisation and Effect of Probiotic Intervention

The human gastrointestinal (GI) microbiota is a complex ecosystem that lives in symbiosis with its host. The growing awareness of the importance of the microbiota to the host as well as the development of culture-free laboratory techniques and computational methods has enormously expanded our knowledge of this microbial community. Irritable bowel syndrome (IBS) is a common functional bowel disorder affecting up to a fifth of the Western population. To date, IBS diagnosis has been based on GI symptoms and the exclusion of organic diseases. The GI microbiota has been found to be altered in this syndrome and probiotics can alleviate the symptoms, although clear links between the symptoms and the microbiota have not been demonstrated. The aim of the present work was to characterise IBS related alterations in the intestinal microbiota, their relation to IBS symptoms and their responsiveness to probiotic theraphy. In this thesis research, the healthy human microbiota was characterised by cloning and sequencing 16S rRNA genes from a faecal microbial community DNA pool that was first profiled and fractionated according to its guanine and cytosine content (%G+C). The most noticeable finding was that the high G+C Gram-positive bacteria (the phylum Actinobacteria) were more abundant compared to a corresponding library constructed from the unfractionated DNA pool sample. Previous molecular analyses of the gut microbiota have also shown comparatively low amounts of high G+C bacteria. Furthermore, the %G+C profiling approach was applied to a sample constructed of faecal DNA from diarrhea-predominant IBS (IBS-D) subjects. The phylogenetic microbial community comparison performed for healthy and IBS-D sequence libraries revealed that the IBS-D sample was rich in representatives of the phyla Firmicutes and Proteobacteria whereas Actinobacteria and Bacteroidetes were abundant in the healthy subjects. The family Lachnospiraceae within the Firmicutes was especially prevalent in the IBS-D sample. Moreover, associations of the GI microbiota with intestinal symptoms and the quality of life (QOL) were investigated, as well as the effect of probiotics on these factors. The microbial targets that were analysed with the quantitative real-time polymerase chain reaction (qPCR) in this study were phylotypes (species definition according to 16S rRNA gene sequence similarity) previously associated with either health or IBS. With a set of samples, the presence or abundance of a phylotype that had 94% 16S rRNA gene sequence similarity to Ruminococcus torques (R. torques 94%) was shown to be associated with the severity of IBS symptoms. The qPCR analyses for selected phylotypes were also applied to samples from a six-month probiotic intervention with a mixture of Lactobacillus rhamnosus GG, L. rhamnosus Lc705, Propionibacterium freudenreichii ssp. shermanii JS and Bifidobacterium breve Bb99. The intervention had been previously reported to alleviate IBS symptoms, but no associations with the analysed microbiota representatives were shown. However, with the phylotype-specific assays applied here, the abundance of the R. torques 94% -phylotype was shown to be lowered in the probiotic-receiving group during the probiotic supplementation, whereas a Clostridium thermosuccinogenes 85% phylotype, previously associated with a healthy microbiota, was found to be increased compared to the placebo group. To conclude, with the combination of methods applied, higher abundance of Actinobacteria was detected in the healthy gut than found in previous studies, and significant phylum-level microbiota alterations could be shown in IBS-D. Thus, the results of this study provide a detailed overview of the human GI microbiota in healthy subjects and in subjects with IBS. Furthermore, the IBS symptoms were linked to a particular clostridial phylotype, and probiotic supplementation was demonstrated to alter the GI microbiota towards a healthier state with regard to this and an additional bacterial phylotype. For the first time, distinct phylotype-level alterations in the microbiota were linked to IBS symptoms and shown to respond to probiotic therapy.

Jahn-Teller effect induced phase transitions in CsCuCl3

Occurence of the three Jahn-Teller effect induced phase transitions of CsCuCl3 at 423, 510 and 535 K has been established and the nature of the transitions examined by X-ray crystallography, far infrared spectroscopy and other techniques.

Growth Kinetics of ZnO Nanocrystals in the Presence of a Base: Effect of the Size of the Alkali Cation

Following an earlier study (J. Am. Chem Soc. 2007, 129, 4470) describing a very unusual growth kinetics of ZnO nanoparticles, we critically evaluate here the proposed mechanism involving a crucial role of the alkali base ion in controlling the growth of ZnO nanoparticles using other alkali bases, namely, LiOH and KOH. While confirming the earlier conclusion of the growth of ZnO nanoparticles being hindered by an effective passivating layer of cations present in the reaction mixture and thereby generalizing this phenomenon, present experimental data reveal an intriguing nonmonotonic dependence of the passivation efficacy on the ionic size of the alkali base ion. This unexpected behavior is rationalized on the basis of two opposing factors: (a) solvated cationic radii and (b) dissociation constant of the base.

Effect of HCl on the adsorption of oxygen on Cu(110) surface: An eels study

Oxygen is shown to adsorb molecularly on a clean Cu(110) surface at 80 K and dissociate around 150 K forming atomic oxygen. Adsorption of oxygen on an HCl covered surface at low temperatures results in the formation of adsorbed hydroxyl groups and water in addition to adsorbed molecular oxygen. The molecular oxygen species is stable up to 190 K on the HCl covered surface.

Effect of morphology and particle size on the ionic conductivities of composite solid electrolytes

A model incorporating the surface conductivity and morphology of the composite solid electrolytes is envisaged to explain their conduction behaviour. The conductivity data on LinX−50 m/o Al2O3 (X = F−, Cl−, Br−, CO32−, SO42−, PO43−) composites prepared by thermal decomposition of LinX·2nAl(OH)3·mH2O salts and Li2SO4−A (A=Al2O3, CeO2, Y2O3, Yb2O3, Zr2O3, ZrO2 and BaTiO3) composites prepared by mechanical mixing of the components are examined in the light of this model. It is surmised that the particle size of both the dispersoids and the hosts not only influence the ionic conductivity of the host matrix but also affect its bulk properties.

Comparison of the effect of processing parameters and degradation on the DC and microwave properties of thin films and polycrystalline bulk high-Tc superconducting materials

The sharp increase in microwave power loss (the reverse of what has previously been reported) at the transition temperature in high-Tc superconducting systems such as YBaCu oxide (polycrystalline bulk and thin films obtained by the laser ablation technique) and BiPbSrCaCu oxide is reported. The differences between DC resistivity ( rho ) and the microwave power loss (related to microwave surface resistance) are analysed from the data obtained by a simultaneous measurement set-up. The influence of various parameters, such as preparation conditions, thickness and aging of the sample and the probing frequency (6-18 GHz), on the variation of microwave power loss with temperature is outlined.

Effect of Sorbate-Zeolite Interaction on Cluster Lifetime and Size of Sorbates: Xe in NaY

Molecular dynamics calculations are reported for Xe in sodium Y zeolite with varying strengths of sorbate-zeolite dispersion interaction. In the absence of any dispersion interaction between the sorbate and the zeolite, the presence of the zeolite has a purely geometrical role. Increase in the strength of the sorbate-zeolite interaction increases the monomer population and decreases the population of dimers and higher sized clusters. The lifetime of the monomers as well as dimers increases with the strength of the dispersion interaction. The observed variations in the lifetime and the population of the different sized clusters is explained in terms of the changes in the potential energy surface caused by the increase in the strength of the dispersion interaction.

Solvent effect on the spectroscopic properties of 6MAMC and 7MAMC

The absorption and emission spectra of two dyes namely 6MAMC and 7MAMC have been recorded at room temperature in solvents of different polarities. The ground-state dipole moments (mu(g)) of these two were determined experimentally by Guggenheim method and were compared with theoretical values obtained using quantum chemical method. The exited state (mu(e))dipole moments were estimated from Lippert's, Bakhshiev's and Chamma-Viallet's equations by using the variation of the Stokes shift with the solvent dielectric constant and refractive index. The ground and excited-state dipole moments were calculated by means of the solvatochromic shift method and also the excited-state dipole moments are determined in combination with ground-state dipole moments. It was observed that dipole moments of excited state were higher than those of the ground state, indicating a substantial redistribution of the pi-electron densities in a more polar excited state for these two dyes. (C) 2010 Elsevier B.V. All rights reserved.

A discrete state perspective of manipulator workspaces Vorstellungen von diskreten zuständen von manipulator-arbeitsräumen

The finite resolution of joint drives or sensors imparts a discrete nature to the joints of a manipulator. Because of this an arbitrary point in the workspace cannot be reached without error even in ideal mechanical environment. This paper investigates the effect of this discrete nature of the joints on the accuracy of performance of a manipulator and develops a method to select the joint states to reach a point with least error. It is shown that the configuration leading to least error cannot, in general, be found from configuration space, especially when there is large variation in the link lengths or joint resolutions or both. The anomaly becomes severe when the gross motion of the end-effector approaches the local resolution of the workspace. The paper also shows how to distinguish two workspaces which may be identical so far as the boundary points are concerned, taking the joint resolutions into account. Finally, the concepts have been extended to define continuous space global and local performance indices for general multi degree of freedom manipulators.

Effect of Li+-ion on enhancement of photoluminescence in Gd2O3:Eu3+ nanophosphors prepared by combustion technique

Gd2O3:Eu3+ (4 mol%) nanophosphor co-doped with Li+ ions have been synthesized by low-temperature solution combustion technique in a short time. Powder X-ray diffractometer (PXRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), UV-VIS and photoluminescence (PL) techniques have been employed to characterize the synthesized nanoparticles. It is found that the lattice of Gd2O3:Eu3+ phosphor transforms from monoclinic to cubic as the Li+-ions are doped. Upon 254 nm excitation, the phosphor showed characteristic luminescence D-5(0) -> F-7(J) (J= 0-4) of the Eu3+ ions. The electronic transition located at 626 nm (D-5(0) -> F-7(2)) of Eu3+ ions was stronger than the magnetic dipole transition located at 595 nm (D-5(0) -> F-7(1)). Furthermore, the effects of the Li+ co-doping as well as calcinations temperature on the PL properties have been studied. The results show that incorporation of Li+ ions in Gd2O3:Eu3+ lattice could induce a remarkable improvement of their PL intensity. The emission intensity was observed to be enhanced four times than that of with out Li+-doped Gd2O3:Eu3+. (C) 2010 Elsevier B.V. All rights reserved,

Dynamics of zeolite cage and its effect on the diffusion properties of sorbate: persistence of diffusion anomaly in NaA zeolite

Recent computer simulations on zeolites Y and A have found that the diffusion coefficient and the rate of intercage diffusion exhibit, apart from a linear dependence on the reciprocal of the square of the sorbate diameter, an anomalous peak as sorbate diameter approaches the window diameter. Here we report molecular dynamics simulations of zeolite NaA incorporating framework flexibility as a function of sorbate diameter in order to verify the existence of anomalous diffusion. Results suggest persistence of anomalous diffusion or ring effect. This suggests that the anomalous behavior is a general effect characteristic of zeolites Y and A. The barrier for diffusion across the eight-ring window is seen to be negative and is found to decrease with sorbate size. The effect of sorbate on the cage motion has also been investigated. Results suggest that the window expands during intercage migration only if the sorbate size is comparable to the window diameter. Flexible cage simulations yield a higher value for the diffusion coefficient and also the rate of intercage diffusion. This increase has been shown to be due to an increase in the intercage diffusions via the centralized diffusion mode rather than the surface-mediated mode. It is shown that this increase arises from an increase in the single particle density distribution in the region near the cage center.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.