Structure and dynamics of a gene network model incorporating small RNAs

As advances in molecular biology continue to reveal additional layers of complexity in gene regulation, computational models need to incorporate additional features to explore the implications of new theories and hypotheses. It has recently been suggested that eukaryotic organisms owe their phenotypic complexity and diversity to the exploitation of small RNAs as signalling molecules. Previous models of genetic systems are, for several reasons, inadequate to investigate this theory. In this study, we present an artificial genome model of genetic regulatory networks based upon previous work by Torsten Reil, and demonstrate how this model generates networks with biologically plausible structural and dynamic properties. We also extend the model to explore the implications of incorporating regulation by small RNA molecules in a gene network. We demonstrate how, using these signals, highly connected networks can display dynamics that are more stable than expected given their level of connectivity.

Effects of cation substitutions on the physical properties of M2M1T2O6 pyroxenes

In this PhD study, the effects of the cation substitutions on the physical properties of pyroxenes have been discussed. The results of this work extend the knowledge on pyroxenes with different chemical compositions. These properties might be used in the development of ceramic pigments, advanced materials and for the mineralogical phase identification. First of all, the crystallographic differences between Ge and Si pyroxenes have been examined. The structure of C2/c Ca rich Ge clinopyroxenes is very close to the low pressure C2/c structural configuration found in Ca-rich Si-pyroxenes. The shear of the unit cell is very similar, and the difference between a Ge end member and the corresponding Si-rich one is less than 1°. Instead, a remarkable difference exists between Ca-poor Si and Ge clinopyroxenes. First, Ca-poor Ge pyroxenes do not display a P21/c symmetry, but retain the C2/c symmetry; second, the observed C2/c structure shows, at room pressure, the configuration with highly kinked tetrahedral chains characteristic of the high pressure C2/c symmetry of Si Ca-poor pyroxenes. In orthopyroxenes, with Pbca symmetry, Ge-pyroxenes have volume larger than Si-pyroxenes. Samples along the system CaCoGe2O6 - CoCoGe2O6 have been synthesized at three different temperatures: 1050 °C, 1200 °C and 1250 °C. The aim of these solid state syntheses was to obtain a solid solution at ambient pressure, since the analogues Si-system needs high pressure. Unfortunately, very limited solution occurs because the structure forms of the two end member (high temperature for CaCoGe2O6 and high pressure CoCoGe2O6) are incompatible. The phase diagram of this system has been sketched and compared to that of Si. The cobalt end member (CoCoGe2O6) is stable at ambient pressure in two symmetries: at 1050 °C C2/c and 1200 °C Pbca. The impurity phase formed during these experiments is cobalt spinel. Raman spectroscopy has been used to investigate the vibrational properties of Ca-pyroxenes CaCoGe2O6, CaMgGe2O6, CaMgSi2O6 and CaCoSi2O6. A comparison between silicate and germanate pyroxenes shows significant changes in peak positions of the corresponding modes caused mainly by the difference of the Ge-Si atomic weight along with the distortion and compression of the coordination polyhedra. Red shift in Raman spectra of germanates has been calculated by a rough scale factor calculated by a simple harmonic oscillator model, considering the different bond lengths for 4-coordinated Si ~ 1.60- 1.65 Å vs Ge–O distance ~1.70 - 1.80 Å. The Raman spectra of CaMgGe2O6 and CaCoGe2O6 have been classified, in analogy with silicate (Wang et al., 2001) counterparts, in different ranges: - R1 (880-640 cm-1): strong T-O stretching modes of Ge and non-bridging O1 and O2 atoms within the GeO4 tetrahedron; - R2 (640-480 cm-1): stretching/bending modes of Ge-Obr-Ge bonds (chain stretching and chain bending); - R4 (480-360 cm-1): O-Ge-O vibrations; - R3 (360-240 cm-1): motions of the cations in M2 and M1 sites correlated with tetrahedral chain motion and tilting tetrahedra; - R5 (below 240 cm-1): lattice modes. The largest shift with respect to CaMgSi2O6 - CaCoSi2O6 is shown by the T-O stretching and chain modes. High-pressure Raman spectroscopy (up to about 8 GPa) on the same samples of Ca-pyroxenes using an ETH-type diamond anvil cell shows no phase transition within the P-ranges investigated, as all the peak positions vary linearly as a function of pressure. Our data confirm previous experimental findings on Si-diopside (Chopelas and Serghiou, 2000). In the investigated samples, all the Raman peaks shift upon compression, but the major changes in wavenumber with pressure are attributed to the chain bending (Ge-Obr-Ge bonds) and tetrahedra stretching modes (Ge-Onbr). Upon compression, the kinking angle, the bond lengths and T-T distances between tetrahedra decrease and consequently the wavenumber of the bending chain mode and tetrahedra stretching mode increases. Ge-pyroxenes show the higher P-induced peak-position shifts, being more compressible than corresponding silicates. The vibrational properties of CaM2+Ge2O6 (M2+ =Mg, Mn, Fe, Co, Ni, Zn) are reported for the first time. The wavenumber of Ge-Obr-Ge bending modes decreases linearly with increasing ionic radius of the M1 cation. No simple correlation has been found with M1 atomic mass or size or crystallographic parameters for the peak at ~850 cm-1 and in the low wavenumber regions. The magnetic properties of the system CaCoSi2O6 - CoCoSi2O6 have been investigated by magnetometry. The join is always characterized by 1 a.p.f.u. of cobalt in M1 site and this causes a pure collinear antiferromagnetic behaviour of the intra-chain superexchange interaction involving Co ions detected in all the measurements, while the magnetic order developed by the cobalt ions in M2 site (intra-chain) is affected by weak ferromagnetism, due to the non-collinearity of their antiferromagnetic interaction. In magnetically ordered systems, this non-collinearity effect promotes a spin canting of anti-parallel aligned magnetic moments and thus is a source of weak ferromagnetic behaviour in an antiferromagnetic. The weak ferromagnetism can be observed only for the samples with Co content higher than 0.5 a.p.f.u. in M2, when the concentration is sufficiently high to create a long range order along the M2 chain which is magnetically independent of M1 chain. The ferromagnetism was detected both in the M(T) at 10 Oe and M(H).

Vibrational dynamics and structure of natural feldspars

The present study gives a contribution to the knowledge on the Na-feldspar and plagioclases, extending the database of the Raman spectra of plagioclases with different chemical compositions and structural orders. This information may be used for the future planetary explorations by “rovers”, for the investigation of ceramics nanocrystal materials and for the mineralogical phase identification in sediments. Na-feldspar and plagioclase solid solution have been investigated by Raman spectroscopy in order to determine the relationships between the vibrational changes and the plagioclase crystal chemistry and structure. We focused on the Raman micro-spectroscopy technique, being a non-destructive method, suited for contactless analysis with high spatial resolution. Chemical and structural analyses have been performed on natural samples to test the usefulness of Raman spectroscopy as a tool in the study of the pressure-induced structural deformations, the disordering processes due to change in the Al-Si distribution in the tetrahedral sites and, finally, in the determination of the anorthitic content (Anx) in plagioclase minerals. All the predicted 39 Ag Raman active modes have been identified and assigned to specific patterns of atomic vibrational motion. A detailed comparison between experimental and computed Raman spectra has been performed and previous assignments have been revised, solving some discrepancies reported in recent literature. The ab initio calculation at the hybrid HF/DFT level with the WC1LYP Hamiltonian has proven to give excellent agreement between calculated and experimentally measured Raman wavenumbers and intensities in triclinic minerals. A short digression on the 36 infrared active modes of Na-feldspar has been done too. The identification of all 39 computed Raman modes in the experimentally measured spectra of the fully ordered Na-feldspar, known as low albite, along with the detailed description of each vibrational mode, has been essential to extend the comparative analysis to the high pressure and high temperature structural forms of albite, which reflect the physical–chemical conditions of the hosting rocks. The understanding of feldspar structure response to pressure and temperature is crucial in order to constrain crustal behaviour. The compressional behaviour of the Na-feldspar has been investigated for the first time by Raman spectroscopy. The absence of phase transitions and the occurrence of two secondary compression mechanisms acting at different pressures have been confirmed. Moreover, Raman data suggest that the internal structural changes are confined to a small pressure interval, localized around 6 GPa, not spread out from 4 to 8 GPa as suggested by previous X-rays studies on elasticity. The dominant compression mechanisms act via tetrahedral tilting, while the T-O bond lengths remain nearly constant at moderate compressional regimes. At the spectroscopic level, this leads to the strong pressure dependencies of T-O-T bending modes, as found for the four modes at 478, 508, 578 and 815 cm-1. The Al-Si distribution in the tetrahedral sites affects also the Raman spectrum of Na-feldspar. In particular, peak broadening is more sensitive than peak position to changes in the degree of order. Raman spectroscopy is found to be a good probe for local ordering, in particular being sensitive to the first annealing steps, when the macroscopic order parameter is still high. Even though Raman data are scattered and there are outliers in the estimated values of the degree of order, the average peak linewidths of the Na-feldspar characteristic doublet band, labelled here as υa and υb, as a function of the order parameter Qod show interesting trends: both peak linewidths linearly increase until saturation. From Qod values lower than 0.6, peak broadening is no more affected by the Al-Si distribution. Moreover, the disordering process is found to be heterogeneous. SC-XRD and Raman data have suggested an inter-crystalline inhomogeneity of the samples, i.e., the presence of regions with different defect density on the micrometric scale. Finally, the influence of Ca-Na substitution in the plagioclase Raman spectra has been investigated. Raman spectra have been collected on a series of well characterized natural, low structural plagioclases. The variations of the Raman modes as a function of the chemical composition and the structural order have been determined. The number of the observed Raman bands at each composition gives information about the unit-cell symmetry: moving away from the C1 structures, the number of the Raman bands enhances, as the number of formula units in the unit cell increases. The modification from an “albite-like” Raman spectrum to a more “anorthite-like” spectrum occurs from sample An78 onwards, which coincides with the appearance of c reflections in the diffraction patterns of the samples. The evolution of the Raman bands υa and υb displays two changes in slope at ~An45 and ~An75: the first one occurs between e2 and e1 plagioclases, the latter separates e1 and I1 plagioclases with only b reflections in their diffraction patterns from I1 and P1 samples having b and c reflections too. The first variation represents exactly the e2→e1 phase transitions, whereas the second one corresponds in good approximation to the C1→I1 transition, which has been determined at ~An70 by previous works. The I1→P1 phase transition in the anorthite-rich side of the solid solution is not highlighted in the collected Raman spectra. Variations in peak broadening provide insights into the behaviour of the order parameter on a local scale, suggesting an increase in the structural disorder within the solid solution, as the structures have to incorporate more Al atoms to balance the change from monovalent to divalent cations. All the information acquired on these natural plagioclases has been used to produce a protocol able to give a preliminary estimation of the chemical composition of an unknown plagioclase from its Raman spectrum. Two calibration curves, one for albite-rich plagioclases and the other one for the anorthite-rich plagioclases, have been proposed by relating the peak linewidth of the most intense Raman band υa and the An content. It has been pointed out that the dependence of the composition from the linewidth can be obtained only for low structural plagioclases with a degree of order not far away from the references. The proposed tool has been tested on three mineralogical samples, two of meteoric origin and one of volcanic origin. Chemical compositions by Raman spectroscopy compare well, within an error of about 10%, with those obtained by elemental techniques. Further analyses on plagioclases with unknown composition will be necessary to validate the suggested method and introduce it as routine tool for the determination of the chemical composition from Raman data in planetary missions.

Incorporation of N-heterocyclic cations into proteins with a highly directed chemical modification

N-Heterocyclic cations are incorporated into proteins using 5-(2-bromoethyl)phenanthridinium bromide, which selectively reacts with either cysteine or lysine residues, resulting in ethylphenanthridinium (Phen) or highly stable cyclised dihydro-imidazo-phenanthridinium (DIP) adducts respectively; these modifications have been found to manipulate the observed structure of lysozyme and bovine serum albumin by AFM.

Functionalisation of polymers: reactive processing, structure and performance characteristics

The main aim of this work was to study the effect of two comonomers, trimethylolpropane trimethacrylate (TRIS) and divinylbenzene (DVB) on the nature and efficiency of grafting of two different monomers, glycidyl methacrylate (GMA) and maleic anhydride (MA) on polypropylene (P) and on natural rubber (NR) using reactive processing methods. Four different peroxides, benzoyl peroxide (BPO), dicumyl peroxide (DCP), 2,5-dimethyl-2,5-bis-(tert-butyl peroxy) hexane (t-101), and 1,1-di(tert-butylperoxy)-3,3,5-trimethyl cyclohexene (T-29B90) were examined as free radical initiators. An appropriate methodology was established and chemical composition and reactive processing parameters were examined and optimised. It was found that in the absence of the coagents DVB and TRIS, the grafting degree of GMA and MA increased with increasing peroxide concentration, but the level of grafting was low and the homopolymerisaton of GMA and the crosslinking of NR or chain scission of PP were identified as the main side reactions that competed with the desired grafting reaction in the polymers. At high concentrations of the peroxide T-101 (>0.02 mr) cross linking of NR and chain scission of PP became dominant and unacceptable. An attempt to add a reactive coagent, e.g. TRIS during grafting of GMA on natural rubber resulted in excessive crosslinking because of the very high reactivity of this comonomer with the C=C of the rubber. Therefore, the use of any multifunctional and highly reactive coagent such as TRIS, could not be applied in the grafting of GAM onto natural rubber. In the case of PP, however, the use of TRIS and DVB was shown to greatly enhance the grafting degree and reduce the chain scission with very little extent of monomer homopolymerisation taking place. The results showed that the grafting degree was increased with increasing GMA and MA concentrations. It was also found that T-101 was a suitable peroxide to initiate the grafting reaction of these monomers on NR and PP and the optimum temperature for this peroxide was =160°C. A very preliminary work was also conducted on the use of the functionalised-PP (f-PP) in the absence and presence of the two comonomers (f-PP-DVB or f-PP-TRIS) for the purpose of compatibilising PP-PBT blends through reactive blending. Examination of the morphology of the blends suggested that an effective compatibilisation has been achieved when using f-PP-DVB and f-PP-TRIS, however more work is required in this area.

The development of a multi-function computer-assisted instruction system using a hierarchical database structure as the lesson compendium.

Computer-Based Learning systems of one sort or another have been in existence for almost 20 years, but they have yet to achieve real credibility within Commerce, Industry or Education. A variety of reasons could be postulated for this, typically: - cost - complexity - inefficiency - inflexibility - tedium Obviously different systems deserve different levels and types of criticism, but it still remains true that Computer-Based Learning (CBL) is falling significantly short of its potential. Experience of a small, but highly successful CBL system within a large, geographically distributed industry (the National Coal Board) prompted an investigation into currently available packages, the original intention being to purchase the most suitable software and run it on existing computer hardware, alongside existing software systems. It became apparent that none of the available CBL packages were suitable, and a decision was taken to develop an in-house Computer-Assisted Instruction system according to the following criteria: - cheap to run; - easy to author course material; - easy to use; - requires no computing knowledge to use (as either an author or student) ; - efficient in the use of computer resources; - has a comprehensive range of facilities at all levels. This thesis describes the initial investigation, resultant observations and the design, development and implementation of the SCHOOL system. One of the principal characteristics c£ SCHOOL is that it uses a hierarchical database structure for the storage of course material - thereby providing inherently a great deal of the power, flexibility and efficiency originally required. Trials using the SCHOOL system on IBM 303X series equipment are also detailed, along with proposed and current development work on what is essentially an operational CBL system within a large-scale Industrial environment.

The growth, structure and properties of sputtered barium titanate thin films

The design and construction of a sputtering system for the deposition of barium titanate thin films is described. The growth and structure of barium titanate films deposited on a variety of substrates including amorphous carbon fi1ms, potassium bromide single crystals, and polycrystalline gold films has been studied. Films deposited on all substrates at room temperature were amorphous. Polycrystalline titanate films were formed on polycrystalline and amorphous substrates at temperatures above 450°C while films with a pronounced texture could be expitaxially deposited on single crystal potassium bromide above a temperature of only 200°C. Results of dielectric measurements made on the films are reported. Amorphous films were highly insulating (resistivities ~1014 ohm.cm with dielectric constants of between 10 and 20.

Ordered mixing of drugs with particulate excipients

A novel direct compression tableting excipient has been made by recrystallisation of lactose. The particles produced had high porosity, high specific surface area and high surface roughness. The resistance to segregation of ordered mixes formed between a model drug; potassium chloride and the excipients recrystallised lactose, spray crystallised maltose-dextrose (Emdexl and a direct compacting sugar (Dipac) was studied using a vibrational segregation model. The highly porous excipients, Emdex and recrystallised lactose formed ordered mixes which did not segregate even at high accelerations and low frequencies whereas the relatively smooth excipient, Dipac, displayed marked segregation in most vibration conditions. The vibrations were related to practical conditions measured in pharmaceutical process machinery. The time required to form an ordered mix was inversely related to the stability of the mix when subjected to vibration. An ultracentrifuge technique was developed to determine the interparticle adhesion forces holding drug and excipient particles together as ordered units. Excipient powders such as Emdex and recrystallised lactose, which formed non-segregating ordered mixes, had high interparticle adhesion forces. Other ordered mixes that segregated when subjected to different vibration conditions were found to have large quantities of weekly-bound drug particles; such mixes included those with Dipac as the carrier excipient as well as those containing a high concentration of drug. The electrostatic properties of different drug and excipient powders were studied using a Faraday well and an electrometer. Excipient powders such as Emdex and recrystallised lactose which formed stable ordered mixes also had a widely different surface charge in comparison with drug particles, whereas Dipac had a similar surface charge to the drug particles and formed unstable ordered mixes. A specially constructed triboelectric charging apparatus based on an air cyclone was developed to increase the affinity of drug particles for different excipient particles. Using triboelectrification to increase the interparticle adhesion forces, the segregation tendencies of unstable ordered mixes were greatly reduced. The stability of ordered mixes is shown to be related to both the surface physical characteristics and the surface electrical properties of the constituent carrier (excipientl particles.

Schematic structure and the modulation of propositions in economics forecasting text

Working within the framework of the branch of Linguistics known as discourse analysis, and more specifically within the current approach of genre analysis, this thesis presents an analysis of the English of economic forecasting. The language of economic forecasting is highly specialised and follows certain conventions of structure and style. This research project identifies these characteristics and explains them in terms of their communicative function. The work is based on a corpus of texts published in economic reports and surveys by major corporate bodies. These documents are targeted at an international expert readership familiar with this genre. The data is analysed at two broad levels: firstly, the macro-level of text structure which is described in terms of schema-theory, a currently influential model of analysis, and, secondly, the micro-level of authors' strategies for modulating the predictions which form the key move in the forecasting schema. The thesis aims to contribute to the newly developing field of genre analysis in a number of ways: firstly, by a coverage of a hitherto neglected but intrinsically interesting and important genre (Economic Forecasting); secondly, by testing the applicability of existing models of analysis at the level of schematic structure and proposing a genre-specific model; thirdly by offering insights into the nature of modulation of propositions which is often broadly classified as `hedging' or `modality', and which has been recently described as lq`an area for prolonged fieldwork'. This phenomenon is shown to be a key feature of this particular genre. It is suggested that this thesis, in addition to its contribution to the theory of genre analysis, provides a useful basis for work by teachers of English for Economics, an important area of English for Specific Purposes.

An efficient route to highly organized, tunable macroporous-mesoporous alumina

(Figure Presented) Organized macroporous-mesoporous alumina can be obtained via a dual-templating approach. Monodispersed polystyrene beads promote macropore formation, while a P123 surfactant templating agent drives the formation of ordered hexagonal mesopores throughout the alumina framework. These well-defined pore networks coexist over a wide range of temperatures and macropore sizes. © 2009 American Chemical Society.

Effects of rare-earth co-doping on the local structure of rare-earth phosphate glasses using high and low energy X-ray diffraction

Rare-earth co-doping in inorganic materials has a long-held tradition of facilitating highly desirable optoelectronic properties for their application to the laser industry. This study concentrates specifically on rare-earth phosphate glasses, (R2O3)x(R'2O3)y(P2O5)1-(x+y), where (R, R') denotes (Ce, Er) or (La, Nd) co-doping and the total rare-earth composition corresponds to a range between metaphosphate, RP3O9, and ultraphosphate, RP5O14. Thereupon, the effects of rare-earth co-doping on the local structure are assessed at the atomic level. Pair-distribution function analysis of high-energy X-ray diffraction data (Qmax = 28 Å-1) is employed to make this assessment. Results reveal a stark structural invariance to rare-earth co-doping which bears testament to the open-framework and rigid nature of these glasses. A range of desirable attributes of these glasses unfold from this finding; in particular, a structural simplicity that will enable facile molecular engineering of rare-earth phosphate glasses with 'dial-up' lasing properties. When considered together with other factors, this finding also demonstrates additional prospects for these co-doped rare-earth phosphate glasses in nuclear waste storage applications. This study also reveals, for the first time, the ability to distinguish between P-O and PO bonding in these rare-earth phosphate glasses from X-ray diffraction data in a fully quantitative manner. Complementary analysis of high-energy X-ray diffraction data on single rare-earth phosphate glasses of similar rare-earth composition to the co-doped materials is also presented in this context. In a technical sense, all high-energy X-ray diffraction data on these glasses are compared with analogous low-energy diffraction data; their salient differences reveal distinct advantages of high-energy X-ray diffraction data for the study of amorphous materials. © 2013 The Owner Societies.

Structure-reactivity correlations in the selective aerobic oxidation of cinnamyl alcohol:in situ XAFS

The structural evolution of a Pd/C catalyst during the liquid phase selective aerobic oxidation of cinnamyl alcohol has been followed by in situ XAFS and XPS. The fresh catalyst comprised highly dispersed, heavily oxidised Pd particles. Cinnamyl alcohol oxidation resulted in the rapid reduction of surface palladium oxide and a small degree of concomitant particle growth. These structural changes coincided with a large drop in catalytic activity. Prereduced Pd/C exhibited a significantly lower initial oxidation rate demonstrating the importance of surface metal oxide in effecting catalytic oxidation. Use of a Pd black model system confirmed that the oxide→metal transformation was the cause, and not result, of catalyst deactivation.

Highly sensitive temperature and strain sensors based on all-fiber 45°-TFG Lyot filter

We demonstrate highly sensitive temperature and strain sensors based on an all-fiber Lyot filter structure, which is formed by concatenating two 45°-TFGs (tilted fiber gratings) with a PM fiber cavity. The experiment results show the all-fiber 45°-TFG Lyot filter has very high sensitivity to strain and temperature. The 45°-TFG Lyot filters of two different cavity lengths (18cm and 40 cm) have been evaluated for temperature sensing by heating a section of the cavity from 10°C to 50°C. The experiment results have shown remarkably high temperature sensitivities of 0.616nm/°C for 18cm and 0.31nm/°C for 40cm long cavity filter, respectively. The 18cm long cavity filter has been subjected to strain variations up to around 550μ ε and the filter has exhibited strain sensitivities of 0.02499nm/μ ε and 0.012nm/μ ε for two straining situations, where its cavity middle section of 18cm and 9cm were stretched, respectively. © 2012 SPIE.

The human hippocampus:structure, function and its significance in neuropsychology and disease

This article discusses the structure, anatomical connections, and functions of the hippocampus (HC) of the human brain and its significance in neuropsychology and disease. The HC is concerned with the analysis of highly abstract data derived from all sensory systems but its specific role remains controversial. Hence, there have been three major theories concerning its function, viz., the memory theory, the spatial theory, and the behavioral inhibition system (BIS) theory. The memory theory has its origin in the surgical destruction of the HC, which results in severe anterograde and partial retrograde amnesia. The spatial theory has its origin in the observation that neurons in the HC of animals show activity related to their location within the environment. By contrast, the behavioral inhibition theory suggests that the HC acts as a 'comparator', i.e., it compares current sensory events with expected or predicted events. If a set of expectations continues to be verified then no alteration of behavior occurs. If, however, a 'mismatch' is detected then the HC intervenes by initiating appropriate action by active inhibition of current motor programs and initiation of new data gathering. Understanding the anatomical connections of the hippocampus may lead to a greater understanding of memory, spatial orientation, and states of anxiety in humans. In addition, HC damage is a feature of neurodegenerative diseases such as Alzheimer's disease (AD), dementia with Lewy bodies (DLB), Pick's disease (PiD), and Creutzfeldt-Jakob disease (CJD) and understanding HC function may help to explain the development of clinical dementia in these disorders.