Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli

Translation initiation from the ribosomal P-site is the specialty of the initiator tRNAs (tRNA(fMet)). Presence of the three consecutive G-C base pairs (G29-C41, G30-C40 and G31-C39) in their anticodon stems, a highly conserved feature of the initiator tRNAs across the three kingdoms of life, has been implicated in their preferential binding to the P-site. How this feature is exploited by ribosomes has remained unclear. Using a genetic screen, we have isolated an Escherichia coli strain, carrying a G122D mutation in folD, which allows initiation with the tRNA(fMet) containing mutations in one, two or all the three G-C base pairs. The strain shows a severe deficiency of methionine and S-adenosylmethionine, and lacks nucleoside methylations in rRNA. Targeted mutations in the methyltransferase genes have revealed a connection between the rRNA modifications and the fundamental process of the initiator tRNA selection by the ribosome.

The chemical ecology of seed dispersal in monoecious and dioecious figs

In the nursery pollination system of figs (Ficus, Moraceae), flower-bearing receptacles called syconia breed pollinating wasps and are units of both pollination and seed dispersal. Pollinators and mammalian seed dispersers are attracted to syconia by volatile organic compounds (VOCs). In monoecious figs, syconia produce both wasps and seeds, while in (gyno)dioecious figs, male (gall) fig trees produce wasps and female (seed) fig trees produce seeds. VOCs were collected using dynamic headspace adsorption methods on freshly collected figs from different trees using Super Q® collection traps. VOC profiles were determined using gas chromatography–mass spectrometry (GC–MS).The VOC profile of receptive and dispersal phase figs were clearly different only in the dioecious mammal-dispersed Ficus hispida but not in dioecious bird-dispersed F. exasperata and monoecious bird-dispersed F. tsjahela. The VOC profile of dispersal phase female figs was clearly different from that of male figs only in F. hispida but not in F. exasperata, as predicted from the phenology of syconium production which only in F. hispida overlaps between male and female trees. Greater difference in VOC profile in F. hispida might ensure preferential removal of seed figs by dispersal agents when gall figs are simultaneously available.The VOC profile of only mammal-dispersed female figs of F. hispida had high levels of fatty acid derivatives such as amyl-acetates and 2-heptanone, while monoterpenes, sesquiterpenes and shikimic acid derivatives were predominant in the other syconial types. A bird- and mammal-repellent compound methyl anthranilate occurred only in gall figs of both dioecious species, as expected, since gall figs containing wasp pollinators should not be consumed by dispersal agents.

Sticking and erosion at carbon-containing plasma-facing materials in fusion reactors

Controlled nuclear fusion is one of the most promising sources of energy for the future. Before this goal can be achieved, one must be able to control the enormous energy densities which are present in the core plasma in a fusion reactor. In order to be able to predict the evolution and thereby the lifetime of different plasma facing materials under reactor-relevant conditions, the interaction of atoms and molecules with plasma first wall surfaces have to be studied in detail. In this thesis, the fundamental sticking and erosion processes of carbon-based materials, the nature of hydrocarbon species released from plasma-facing surfaces, and the evolution of the components under cumulative bombardment by atoms and molecules have been investigated by means of molecular dynamics simulations using both analytic potentials and a semi-empirical tight-binding method. The sticking cross-section of CH3 radicals at unsaturated carbon sites at diamond (111) surfaces is observed to decrease with increasing angle of incidence, a dependence which can be described by a simple geometrical model. The simulations furthermore show the sticking cross-section of CH3 radicals to be strongly dependent on the local neighborhood of the unsaturated carbon site. The erosion of amorphous hydrogenated carbon surfaces by helium, neon, and argon ions in combination with hydrogen at energies ranging from 2 to 10 eV is studied using both non-cumulative and cumulative bombardment simulations. The results show no significant differences between sputtering yields obtained from bombardment simulations with different noble gas ions. The final simulation cells from the 5 and 10 eV ion bombardment simulations, however, show marked differences in surface morphology. In further simulations the behavior of amorphous hydrogenated carbon surfaces under bombardment with D^+, D^+2, and D^+3 ions in the energy range from 2 to 30 eV has been investigated. The total chemical sputtering yields indicate that molecular projectiles lead to larger sputtering yields than atomic projectiles. Finally, the effect of hydrogen ion bombardment of both crystalline and amorphous tungsten carbide surfaces is studied. Prolonged bombardment is found to lead to the formation of an amorphous tungsten carbide layer, regardless of the initial structure of the sample. In agreement with experiment, preferential sputtering of carbon is observed in both the cumulative and non-cumulative simulations

Synergistic crystal facet engineering and structural control of WO3 films exhibiting unprecedented photoelectrochemical performance

WO3 nanoplate arrays with (002) oriented facets grown on fluorine doped SnO2 (FTO) glass substrates are tailored by tuning the precursor solution via a facile hydrothermal method. A 2-step hydrothermal method leads to the preferential growth of WO3 film with enriched (002) facets, which exhibits extraordinary photoelectrochemical (PEC) performance with a remarkable photocurrent density of 3.7 mA cm–2 at 1.23 V vs. revisable hydrogen electrode (RHE) under AM 1.5 G illumination without the use of any cocatalyst, corresponding to ~93% of the theoretical photocurrent of WO3. Density functional theory (DFT) calculations together with experimental studies reveal that the enhanced photocatalytic activity and better photo-stability of the WO3 films are attributed to the synergistic effect of highly reactive (002) facet and nanoplate structure which facilitates the photo–induced charge carrier separation and suppresses the formation of peroxo-species. Without the use of oxygen evolution cocatalysts, the excellent PEC performance, demonstrated in this work, by simply tuning crystal facets and nanostructure of pristine WO3 films may open up new opportunities in designing high performance photoanodes for PEC water splitting.

New Strategies for the Enrichment of Metallic Single-Walled Carbon Nanotubes

Enrichment of metallic single-walled carbon nanotubes (SWNTs) has been accomplished by several means, including new extraction and synthetic procedures and by interaction with metal nanoparticles as well as electron donor molecules. In the presence of Fe(CO)(5) the arc discharge method yields nearly pure metallic nanotubes. Fluorous chemistry involving the preferential diazotization of metallic SWNTs offers a good procedure of obtaining the pure metallic species. Interaction of gold or platinum nanoparticles as well as of electron-donor molecules such as aniline and tetrathiafulvalene (TTF) transform semiconducting SWNTs into metallic ones. Raman and electroni spectroscopies provide ideal means to monitor enrichment of metallic SWNTs.

Radiation effects in supported nanoparticles

Nanotechnology applications are entering the market in increasing numbers, nanoparticles being among the main classes of materials used. Particles can be used, e.g., for catalysing chemical reactions, such as is done in car exhaust catalysts today. They can also modify the optical and electronic properties of materials or be used as building blocks for thin film coatings on a variety of surfaces. To develop materials for specific applications, an intricate control of the particle properties, structure, size and shape is required. All these depend on a multitude of factors from methods of synthesis and deposition to post-processing. This thesis addresses the control of nanoparticle structure by low-energy cluster beam deposition and post-synthesis ion irradiation. Cluster deposition in high vacuum offers a method for obtaining precisely controlled cluster-assembled materials with minimal contamination. Due to the clusters small size, however, the cluster-surface interaction may drastically change the cluster properties on deposition. In this thesis, the deposition process of metal and alloy clusters on metallic surfaces is modelled using molecular dynamics simulations, and the mechanisms influencing cluster structure are identified. Two mechanisms, mechanical melting upon deposition and thermally activated dislocation motion, are shown to determine whether a deposited cluster will align epitaxially with its support. The semiconductor industry has used ion irradiation as a tool to modify material properties for decades. Irradiation can be used for doping, patterning surfaces, and inducing chemical ordering in alloys, just to give a few examples. The irradiation response of nanoparticles has, however, remained an almost uncharted territory. Although irradiation effects in nanoparticles embedded inside solid matrices have been studied, almost no work has been done on supported particles. In this thesis, the response of supported nanoparticles is studied systematically for heavy and light ion irradiation. The processes leading to damage production are identified and models are developed for both types of irradiation. In recent experiments, helium irradiation has been shown to induce a phase transformation from multiply twinned to single-crystalline nanoparticles in bimetallic alloys, but the nature of the transition has remained unknown. The alloys for which the effect has been observed are CuAu and FePt. It is shown in this thesis that transient amorphization leads to the observed transition and that while CuAu and FePt do not amorphize upon irradiation in bulk or as thin films, they readily do so as nanoparticles. This is the first time such an effect is demonstrated with supported particles, not embedded in a matrix where mixing is always an issue. An understanding of the above physical processes is essential, if nanoparticles are to be used in applications in an optimal way. This thesis clarifies the mechanisms which control particle morphology, and paves way for the synthesis of nanostructured materials tailored for specific applications.

Pt2+ Dispersed in Ce0.83Ti0.15O2-delta: Significant Improvement in PROX Activity by Ti Substitution in CeO2 in Hydrogen Rich Stream

Pt2+ ion dispersed in CeO2, Ce1-xTixO2-delta and TiO2 have been tested for preferential oxidation of carbon monoxide (PROX) in hydrogen rich stream. It is found that Pt2+ substituted CeO2 and Ce(1-x)TixO(2-delta) in the form of solid solution Ce0.98Pt0.02O2-delta and Ce0.83Ti0.15Pt0.02O2-delta are highly CO selective low temperature PROX catalysts in hydrogen rich stream. Just 15% of Ti substitution in CeO2 improves the overall PROX activity.

A modified least squares algorithm to treat associations in liquid alloys

The associated model for binary systems has been modified to include volume effects and excess entropy arising from preferential interactions between the associate and the free atoms or between the free atoms. Equations for thermodynamic mixing functions have been derived. An optimization procedure using a modified conjugate gradient method has been used to evaluate the enthalpy and entropy interaction energies, the free energy of dissociation of the complex, its temperature dependance and the size of the associate. An expression for the concentration—concentration structure factor [Scc (0)] has been deduced from the modified associated solution model. The analysis has been applied to the thermodynamic mixing functions of liquid Ga-Te alloys at 1120 K, believed to contain Ga2Te3 associates. It is observed that the modified associated solution model incorporating volume effects and terms for the temperature dependance of interaction energies, describes the thermodynamic properties of Ga-Te system satisfactorily.

Structural alteration from non-B to B-form could reflect DNase I hypersensitivity

Preferential cleavage of active genes by DNase I has been correlated with a structurally altered conformation of DNA at the hypersensitive site in chromatin. To have a better understanding of the structural requirements for gene activation as probed by DNase I action, digestability by DNase I of synthetic polynucleotides having the ability to adopt B and non-B conformation (like Z-form) was studied which indicated a marked higher digestability of the B-form of DNA. Left handed Z form present within a natural sequence in supercoiled plasmid also showed marked resistance towards DNase I digestion. We show that alternating purine-pyrimidine sequences adopting Z-conformation exhibit DNAse I foot printing even in a protein free system. The logical deductions from the results indicate that 1) altered structure like Z-DNA is not a favourable substrate for DNase I, 2) both the ends of the alternating purine-pyrimidine insert showed hypersensitivity, 3) B-form with a minor groove of 12-13 A is a more favourable substrate for DNase I than an altered structure, 4) any structure of DNA deviating largely from B form with a capacity to flip over to the B-form are potential targets for the DNase I enzymic probes in naked DNA.

Conformational analysis of the right-hand twisted antiparallel β-Structure

The conformational analysis of a pair of two-linked peptide units in the anti-parallel arrangement is reported here with a view to study the effect of association of one chain with the other. The pair of two-linked peptide units were fixed in space through the hydrogen bonds between them, in accordance with certain hydrogen bond criteria. Model building was undertaken to ascertain whether the proximity of the side-chains could be used to eliminate any one of the right-hand twisted, left-hand twisted or regular β-structures. Stereochemically, it was found possible with all of them. The preference for a right-hand twisted β-structure, however, was indicated by the classical energy calculations. The relevance of the results thus obtained is discussed in the context of the preferential right-hand twist of the β-pleated sheets present in globular proteins. The agreement between the minimum energy conformations obtained for the pair of two-linked peptide units and the globular protein data is also indicated.

Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n

The conformation of (Pro-Gly-Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro-Gly-Phe)n can exist in a partially triple-helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly-R2-R3, in collagen.

Ce0.78Sn0.2Pt0.02O2-delta: A new non-deactivating catalyst for hydrogen production via water-gas shift reaction

We demonstrate the activity of Ce0.78Sn0.2Pt0.02O2-delta, a new catalyst, towards water-gas shift (WGS) reaction. Over 99.5% CO conversion to H-2 is observed at 300 +/- 25 degrees C. Based on different characterization techniques we found that the present catalyst is resistant to deactivation due to carbonate formation and sintering of Pt on the surface when subjected to longer duration of reaction conditions. The catalyst does not require any pre-treatment or activation between start-up/shut-down reaction operations. Formation of side products such as methane, methanol, formaldehyde, coke etc. was not observed under the WGS reaction conditions indicating the high selectivity of the catalyst for H-2. Temperature programmed reduction of the catalyst in hydrogen (H-2-TPR) shows reversible reduction of Ce4+ to Ce3+, Sn4+ to Sn2+ and Pt4+ to Pt-0 oxidation state with oxygen storage capacity (OSC) of 3500 mu mol g(-1) at 80 degrees C. Such high value of OSC indicates the presence of highly activated lattice oxygen. CO oxidation in presence of stoichiometric O-2 shows 100% conversion to CO2 at room temperature. The catalyst also exhibits 100% selectivity for CO2 at room temperature towards preferential oxidation (PROX) of residual CO in presence of excess hydrogen in the feed. (C) 2010 Elsevier B.V. All rights reserved.

Polymeereillä stabiloitu amorfinen formulaatio

Nowadays growing number of new active pharmaceutical ingredients (API) have large molecular weight and are hydrophobic. The energy of their crystal lattice is bigger and polarity has decreased. This leads to weakened solubility and dissolution rate of the drug. These properties can be enhanced for example by amorphization. Amorphous form has the best dissolution rate in the solid state. In the amorphous form drug molecules are randomly arranged, so the energy required to dissolve molecules is lower compared to the crystalline counterpart. The disadvantage of amorphous form is that it is unstable. Amorphous form tends to crystallize. Stability of amorphous form can be enhanced by adding an adjuvant to drug product. Adjuvant is usually a polymer. Polymers prevent crystallization both by forming bonds with API molecules and by steric hindrance. The key thing in stabilizing amorphous form is good miscibility between API and polymer. They have to be mixed in a molecular level so that the polymer is able to prevent crystallization. The aim of this work was to study miscibility of drug and polymer and stability of their dispersion with different analytical methods. Amorphous dispersions were made by rotary evaporator and freeze dryer. Amorphicity was confirmed with X-ray powder diffraction (XRPD) right after preparation. Itraconazole and theophylline were the chosen molecules to be stabilized. Itraconazole was expected to be easier and theophylline more difficult to stabilize. Itraconazole was stabilized with HPMC and theophylline was stabilized with PVP. Miscibility was studied with XRPD and differential scanning calorimetry (DSC). In addition it was studied with polarized light microscope if miscibility was possible to see visually. Dispersions were kept in stressed conditions and the crystallization was analyzed with XRPD. Stability was also examined with isothermal microcalorimetry (IMC). The dispersion of itraconazole and theophylline 40/60 (w/w) was completely miscible. It was proved by linear combination of XRPD results and single glass transition temperature in DSC. Homogenic well mixed film was observed with light microscope. Phase separation was observed with other compositions. Dispersions of theophylline and PVP mixed only partly. Stability of itraconazole dispersions were better than theophylline dispersions which were mixed poorer. So miscibility was important thing considering stability. The results from isothermal microcalorimetry were similar to results from conventional stability studies. Complementary analytical methods should be used when studying miscibility so that the results are more reliable. Light microscope is one method in addition to mostly used XRPD and DSC. Analyzing light microscope photos is quite subjective but it gives an idea of miscibility. Isothermal microcalorimetry can be one option for conventional stability studies. If right conditions can be made where the crystallization is not too fast, it may be possible to predict stability with isothermal microcalorimetry.

Dielectric properties of electron irradiated PbZrO3 thin films

The present paper deals with the study of the effects of electron (8 MeV) irradiation on the dielectric and ferroelectric properties of PbZrO3 thin films grown by sol-gel technique. The films were (0.62 mu m thick) subjected to electron irradiation using Microtron accelerator (delivered dose 80, 100, 120 kGy). The films were well crystallized prior to and after electron irradiation. However, local amorphization was observed after irradiation. There is an appreciable change in the dielectric constant after irradiation with different delivered doses. The dielectric loss showed significant frequency dispersion for both unirradiated and electron irradiated films. T (c) was found to shift towards higher temperature with increasing delivered dose. The effect of radiation induced increase of E >'(T) is related to an internal bias field, which is caused by radiation induced charges trapped at grain boundaries. The double butterfly loop is retained even after electron irradiation to the different delivered doses. The broader hysteresis loop seems to be related to radiation induced charges causing an enhanced space charge polarization. Radiation-induced oxygen vacancies do not change the general shape of the AFE hysteresis loop but they increase P (s) of the hysteresis at the electric field forced AFE to FE phase transition. We attribute the changes in the dielectric properties to the structural defects such as oxygen vacancies and radiation induced charges. The shift in T (C), increase in dielectric constant, broader hysteresis loop, and increase in P (r) can be related to radiation induced charges causing space charge polarization. Double butterfly and hysteresis loops were retained indicative of AFE nature of the films.

Analysis of forest soil chemistry and hydrology with a dynamic model ACIDIC.

In this study we analyze how the ion concentrations in forest soil solution are determined by hydrological and biogeochemical processes. A dynamic model ACIDIC was developed, including processes common to dynamic soil acidification models. The model treats up to eight interacting layers and simulates soil hydrology, transpiration, root water and nutrient uptake, cation exchange, dissolution and reactions of Al hydroxides in solution, and the formation of carbonic acid and its dissociation products. It includes also a possibility to a simultaneous use of preferential and matrix flow paths, enabling the throughfall water to enter the deeper soil layers in macropores without first reacting with the upper layers. Three different combinations of routing the throughfall water via macro- and micropores through the soil profile is presented. The large vertical gradient in the observed total charge was simulated succesfully. According to the simulations, gradient is mostly caused by differences in the intensity of water uptake, sulfate adsorption and organic anion retention at the various depths. The temporal variations in Ca and Mg concentrations were simulated fairly well in all soil layers. For H+, Al and K there were much more variation in the observed than in the simulated concentrations. Flow in macropores is a possible explanation for the apparent disequilibrium of the cation exchange for H+ and K, as the solution H+ and K concentrations have great vertical gradients in soil. The amount of exchangeable H+ increased in the O and E horizons and decreased in the Bs1 and Bs2 horizons, the net change in whole soil profile being a decrease. A large part of the decrease of the exchangeable H+ in the illuvial B horizon was caused by sulfate adsorption. The model produces soil water amounts and solution ion concentrations which are comparable to the measured values, and it can be used in both hydrological and chemical studies of soils.