X-ray scattering study of the effect of hydration on the cross-beta structure of amyloid fibrils

We have investigated the effect of sample hydration on the wide-angle X-ray scattering patterns of amyloid fibrils from two different sources, hen egg white lysozyme (HEWL) and an 11-residue peptide taken from the sequence of transthyretin (TTR105-115). Both samples show an inter-strand reflection at 4.7 Å and an inter-sheet reflection which occurs at 8.8 and 10 Å for TTR105-115 and HEWL fibrils, respectively. The positions, widths, and relative intensities of these reflections are conserved in patterns obtained from dried stalks and hydrated samples over a range of fibril concentrations. In 2D scattering patterns obtained from flow-aligned hydrated samples, the inter-strand and inter-sheet reflections showed, respectively, axial and equatorial alignment relative to the fibril axis, characteristic of the cross-β structure. Our results show that the cross-β structure of the fibrils is not a product of the dehydrating conditions typically employed to produce aligned samples, but is conserved in individual fibrils in hydrated samples under dilute conditions comparable to those associated with other biophysical and spectroscopic techniques. This suggests a structure consisting of a stack of two or more sheets whose interfaces are inaccessible to bulk water.

Determining the effect of asymmetric data on the variogram. I. Underlying asymmetry

Matheron's usual variogram estimator can result in unreliable variograms when data are strongly asymmetric or skewed. Asymmetry in a distribution can arise from a long tail of values in the underlying process or from outliers that belong to another population that contaminate the primary process. This paper examines the effects of underlying asymmetry on the variogram and on the accuracy of prediction, and the second one examines the effects arising from outliers. Standard geostatistical texts suggest ways of dealing with underlying asymmetry; however, this is based on informed intuition rather than detailed investigation. To determine whether the methods generally used to deal with underlying asymmetry are appropriate, the effects of different coefficients of skewness on the shape of the experimental variogram and on the model parameters were investigated. Simulated annealing was used to create normally distributed random fields of different size from variograms with different nugget:sill ratios. These data were then modified to give different degrees of asymmetry and the experimental variogram was computed in each case. The effects of standard data transformations on the form of the variogram were also investigated. Cross-validation was used to assess quantitatively the performance of the different variogram models for kriging. The results showed that the shape of the variogram was affected by the degree of asymmetry, and that the effect increased as the size of data set decreased. Transformations of the data were more effective in reducing the skewness coefficient in the larger sets of data. Cross-validation confirmed that variogram models from transformed data were more suitable for kriging than were those from the raw asymmetric data. The results of this study have implications for the 'standard best practice' in dealing with asymmetry in data for geostatistical analyses. (C) 2007 Elsevier Ltd. All rights reserved.

Salt marsh morphodynamics: An investigation of tidal flows and marsh channel equilibrium

Although numerous field studies have evaluated flow and transport processes in salt marsh channels, the overall role of channels in delivering and removing material from salt marsh platforms is still poorly characterised. In this paper, we consider this issue based on a numerical hydrodynamic model for a prototype marsh system and on a field survey of the cross-sectional geometry of a marsh channel network. Results of the numerical simulations indicate that the channel transfers approximately three times the volume of water that would be estimated from mass balance considerations alone. Marsh platform roughness exerts a significant influence on the partitioning of discharge between the channel and the marsh platform edge, alters flow patterns on the marsh platform due to its effects on channel-to-platform transfer and also controls the timing of peak discharge relative to marsh-edge overtopping. Although peak channel discharges and velocities are associated with the flood tide and marsh inundation, a larger volume of water is transferred by the channel during ebb flows, a portion of which transfer takes place after the tidal height is below the marsh platform. Detailed surveys of the marsh channels crossing a series of transects at Upper Stiffkey Marsh, north Norfolk, England, show that the total channel cross-sectional area increases linearly with catchment area in the inner part of the marsh, which is consistent with the increase in shoreward tidal prism removed by the channels. Toward the marsh edge, however, a deficit in the total cross-sectional area develops, suggesting that discharge partitioning between the marsh channels and the marsh platform edge may also be expressed in the morphology of marsh channel systems.

Analysis of water-level response to rainfall and implications for recharge pathways in the Chalk aquifer, SE England

Water table response to rainfall was investigated at six sites in the Upper, Middle and Lower Chalk of southern England. Daily time series of rainfall and borehole water level were cross-corretated to investigate seasonal variations in groundwater-level response times, based on periods of 3-month duration. The time tags (in days) yielding significant correlations were compared with the average unsaturated zone thickness during each 3-month period. In general, for cases when the unsaturated zone was greater than 18 m thick, the time tag for a significant water-level response increased rapidly once the depth to the water table exceeded a critical value, which varied from site to site. For shallower water tables, a linear relationship between the depth to the water table and the water-level response time was evident. The observed variations in response time can only be partially accounted for using a diffusive model for propagation through the unsaturated matrix, suggesting that some fissure flow was occurring. The majority of rapid responses were observed during the winter/spring recharge period, when the unsaturated zone is thinnest and the unsaturated zone moisture content is highest, and were more likely to occur when the rainfall intensity exceeded 5 mm/day. At some sites, a very rapid response within 24 h of rainfall was observed in addition to the longer term responses even when the unsaturated zone was up to 64 m thick. This response was generally associated with the autumn period. The results of the cross-correlation analysis provide statistical support for the presence of fissure flow and for the contribution of multiple pathways through the unsaturated zone to groundwater recharge. (c) 2006 Elsevier B.V. All rights reserved.

Sonogashira coupling on an extended gold surface in vacuo: reaction of phenylacetylene with iodobenzene on Au(111)

Temperature-programmed reaction measurements supported by scanning tunneling microscopy have shown that phenylacetylene and iodobenzene react on smooth Au(111) under vacuum conditions to yield biphenyl and diphenyldiacetylene, the result of homocoupling of the reactant molecules. They also produce diphenylacetylene, the result of Sonogashira cross-coupling, prototypical of a class of reactions that are of paramount importance in synthetic organic chemistry and whose mechanism remains controversial. Roughened Au(111) is completely inert toward all three reactions, indicating that the availability of crystallographically well-defined adsorption sites is crucially important. High-resolution X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy show that the reactants are initially present as intact, essentially flat-lying molecules and that the temperature threshold for Sonogashira coupling coincides with that for C−I bond scission in the iodobenzene reactant. The fractional-order kinetics and low temperature associated with desorption of the Sonogashira product suggest that the reaction occurs at the boundaries of islands of adsorbed reactants and that its appearance in the gas phase is rate-limited by the surface reaction. These findings demonstrate unambiguously and for the first time that this heterogeneous cross-coupling chemistry is an intrinsic property of extended, metallic pure gold surfaces: no other species, including solvent molecules, basic or charged (ionic) species are necessary to mediate the process.

The component polypeptide chains of bovine insulin nucleate or inhibit aggregation of the parent protein in a conformation-dependent manner

Amyloid fibrils are typically rigid, unbrariched structures with diameters of similar to 10 nm and lengths up to several micrometres, and are associated with more than 20 diseases including Alzheimer's disease and type II diabetes. Insulin is a small, predominantly alpha-helical protein consisting of 51 residues in two disulfide-linked polypeptide chains that readily assembles into amyloid fibrils under conditions of low PH and elevated temperature. We demonstrate here that both the A-chain and the B-chain of insulin are capable of forming amyloid fibrils in isolation under similar conditions, with fibrillar morphologies that differ from those composed of intact insulin. Both the A-chain and B-chain fibrils were found to be able to cross-seed the fibrillization of the parent protein, although these reactions were substantially less efficient than self-seeding with fibrils composed of full-length insulin. In both cases, the cross-seeded fibrils were morphologically distinct from the seeding, material, but shared common characteristics with typical insulin fibrils, including a very similar helical repeat. The broader distribution of heights of the cross-seeded fibrils compared to typical insulin fibrils, however, indicates that their underling protofilament hierarchy may be subtly different. In addition, and remarkably in view of this seeding behavior, the soluble forms of the A-chain and B-chain peptides were found to be capable of inhibiting insulin fibril formation. Studies using mass spectrometry suggest that this behavior might be attributable to complex formation between insulin and the A-chain and B-chain peptides. The finding that the same chemical form of a polypeptide chain in different physical states can either stimulate or inhibit the conversion of a protein into amyloid fibrils sheds new light on the mechanisms underlying fibril formation, fibril strain propagation and amyloid disease initiation and progression. (c) 2006 Elsevier Ltd. All rights reserved.

Mechanical effects of plant cell wall enzymes on xyloglucan/cellulose composites

Xyloglucan-acting enzymes are believed to have effects on type I primary plant cell wall mechanical properties. In order to get a better understanding of these effects, a range of enzymes with different in vitro modes of action were tested against cell wall analogues (bio-composite materials based on Acetobacter xylinus cellulose and xyloglucan). Tomato pericarp xyloglucan endo transglycosylase (tXET) and nasturtium seed xyloglucanase (nXGase) were produced heterologously in Pichia pastoris. Their action against the cell wall analogues was compared with that of a commercial preparation of Trichoderma endo-glucanase (EndoGase). Both 'hydrolytic' enzymes (nXGase and EndoGase) were able to depolymerise not only the cross-link xyloglucan fraction but also the surface-bound fraction. Consequent major changes in cellulose fibril architecture were observed. In mechanical terms, removal of xyloglucan cross-links from composites resulted in increased stiffness (at high strain) and decreased visco-elasticity with similar extensibility. On the other hand, true transglycosylase activity (tXET) did not affect the cellulose/xyloglucan ratio. No change in composite stiffness or extensibility resulted, but a significant increase in creep behaviour was observed in the presence of active tXET. These results provide direct in vitro evidence for the involvement of cell wall xyloglucan-specific enzymes in mechanical changes underlying plant cell wall re-modelling and growth processes. Mechanical consequences of tXET action are shown to be complimentary to those of cucumber expansin.

A case study of intelligent buildings: Manchester stadium

This paper provides a case study of the City of Manchester Stadium based on relevant literatures, based on a comprehensive description of multidisciplinary, cross-sectoral and future-oriented requirements and operations in the design of modern intelligent sports buildings. The successfulness of the City of Manchester Stadium gives constructive experience and knowledge for the building professions including architecture, building structure, building services, construction, and facilities management, etc. In addition, this paper is valuable for developing intelligent sports buildings in China.

Design of mucoadhesive polymeric films based on blends of poly(acrylic acid) and (hydroxypropyl)cellulose

Mixing of aqueous solutions of poly(acrylic acid) and (hydroxypropyl) cellulose results in formation of hydrogen-bonded interpolymer complexes, which precipitate and do not allow preparation of homogeneous polymeric films by casting. In the present work the effect of pH on the complexation between poly(acrylic acid) and (hydroxypropyl)cellulose in solutions and miscibility of these polymers in solid state has been studied. The pH-induced complexation-miscibility-immiscibility transitions in the polymer mixtures have been observed. The optimal conditions for preparation of homogeneous polymeric films based on blends of these polymers have been found, and the possibility of radiation cross-linking of these materials has been demonstrated. Although the gamma-radiation treatment of solid polymeric blends was found to be inefficient, successful cross-linking was achieved by addition of N, N'- methylenebis(acrylamide). The mucoadhesive potential of both soluble and cross-linked films toward porcine buccal mucosa is evaluated. Soluble films adhered to mucosal tissues undergo dissolution within 30-110 min depending on the polymer ratio in the blend. Cross-linked films are retained on the mucosal surface for 10-40 min and then detach.

Alignment of a model amyloid peptide fragment in bulk and at a solid surface

The alignment of model amyloid peptide YYKLVFFC is investigated in bulk and at a solid surface using a range of spectroscopic methods employing polarized radiation. The peptide is based on a core sequence of the amyloid beta (A beta) peptide, KLVFF. The attached tyrosine and cysteine units are exploited to yield information on alignment and possible formation of disulfide or dityrosine links. Polarized Raman spectroscopy on aligned stalks provides information on tyrosine orientation, which complements data from linear dichroism (LD) on aqueous solutions subjected to shear in a Couette cell. LD provides a detailed picture of alignment of peptide strands and aromatic residues and was also used to probe the kinetics of self-assembly. This suggests initial association of phenylalanine residues, followed by subsequent registry of strands and orientation of tyrosine residues. X-ray diffraction (XRD) data from aligned stalks is used to extract orientational order parameters from the 0.48 nm reflection in the cross-beta pattern, from which an orientational distribution function is obtained. X-ray diffraction on solutions subject to capillary flow confirmed orientation in situ at the level of the cross-beta pattern. The information on fibril and tyrosine orientation from polarized Raman spectroscopy is compared with results from NEXAFS experiments on samples prepared as films on silicon. This indicates fibrils are aligned parallel to the surface, with phenyl ring normals perpendicular to the surface. Possible disulfide bridging leading to peptide dimer formation was excluded by Raman spectroscopy, whereas dityrosine formation was probed by fluorescence experiments and was found not to occur except under alkaline conditions. Congo red binding was found not to influence the cross-beta XRD pattern.

An efficient flux difference splitting algorithm for unsteady duct flows of a real gas

A numerical scheme is presented for the solution of the Euler equations of compressible flow of a real gas in a single spatial coordinate. This includes flow in a duct of variable cross-section, as well as flow with slab, cylindrical or spherical symmetry, as well as the case of an ideal gas, and can be useful when testing codes for the two-dimensional equations governing compressible flow of a real gas. The resulting scheme requires an average of the flow variables across the interface between cells, and this average is chosen to be the arithmetic mean for computational efficiency, which is in contrast to the usual “square root” averages found in this type of scheme. The scheme is applied with success to five problems with either slab or cylindrical symmetry and for a number of equations of state. The results compare favourably with the results from other schemes.

Self-assembly of an amyloid peptide fragment–PEG conjugate: lyotropic phase formation and influence of PEG crystallization

The self-assembly of PEGylated peptides containing a modified sequence from the amyloid beta peptide, YYKLVFF, has been studied in aqueous solution. Two PEG molar masses, PEG1k and PEG3k, were used in the conjugates. It is shown that both YYKLVFF–PEG hybrids form fibrils comprising a peptide core and a PEG corona. The fibrils are much longer for YYKLVFF–PEG1k, pointing to an influence of PEG chain length. The beta-sheet secondary structure of the peptide is retained in the conjugate. Lyotropic liquid crystal phases, specifically nematic and hexagonal columnar phases, are formed at sufficiently high concentration. Flow alignment of these mesophases was investigated by small-angle neutron scattering with in situ steady shearing in a Couette cell. On drying, PEG crystallization occurs leading to characteristic peaks in the X-ray diffraction pattern, and to lamellar structures imaged by atomic force microscopy. The X-ray diffraction pattern retains features of the cross-beta pattern from the beta-sheet structure, showing that this is not disrupted by PEG crystallization.

Dynamic shear modulus of isotropic elastomers

We have investigated the dynamic mechanical behavior of two cross-linked polymer networks with very different topologies: one made of backbones randomly linked along their length; the other with fixed-length strands uniformly cross-linked at their ends. The samples were analyzed using oscillatory shear, at very small strains corresponding to the linear regime. This was carried out at a range of frequencies, and at temperatures ranging from the glass plateau, through the glass transition, and well into the rubbery region. Through the glass transition, the data obeyed the time-temperature superposition principle, and could be analyzed using WLF treatment. At higher temperatures, in the rubbery region, the storage modulus was found to deviate from this, taking a value that is independent of frequency. This value increased linearly with temperature, as expected for the entropic rubber elasticity, but with a substantial negative offset inconsistent with straightforward enthalpic effects. Conversely, the loss modulus continued to follow time-temperature superposition, decreasing with increasing temperature, and showing a power-law dependence on frequency.

Untitled (Abstraction of labour time eternal recurrence monad)

An AHRC funded project titled: Picturing ideas? Visualising and Synthesising Ideas as art (2009-10). Outputs including: 4 exhibitions; 4 publications; 3 papers; 2 largescale backlit digital prints; 1 commissioned print. (See Additional Information) ----ABSTRACT: Utilising the virtuality of digital imagery this practice-led project explored the possibility of the cross-articulation between text and image and the bridging or synthesising potential of the visual affect of ideas. A series of digital images were produced 'picturing' or 'visualising' philosophical ideas derived from the writings of the philosopher Giles Deleuze, as remodellings of pre-existing philosophical ideas; developed through dialogues and consultation with specialists in the fields from which the ideas were drawn (philosophy, psychology, film) as well as artists and theorists concerned with ideas of 'mental imagery' and visualisation. Final images were produced as a synthesis (or combination) of these visualisations and presented in the format of large scale, backlit digital prints at a series of prestigious international exhibitions (see details above). Evaluation took the form of a four page illustrated text in Frieze magazine (August 2009) and three papers delivered at University of Ulster, Goldsmiths College of Art and Loughborough University. The project also included the publication of a catalogue essay (EAST 09) and an illustrated poem (in the Dark Monarch publication). A print version of the image was commissioned by Invisible Exports Gallery, New York and subsequently exhibited in The Devos Art Museum, School of Art & Design at Northern Michigan University and in a publication edited by Cedar Lewisohn for Tate Publishing. The project was funded by an AHRC practice-led grant (17K) and Arts Council of England award (1.5K). The outputs, including high profile, publicly accessible exhibitions, prestigious publications and conference papers ensured the dissemination of the research to a wide range of audiences, including scholars/researchers across the arts and humanities engaged in practice-based and interdisciplinary theoretical work (in particular in the fields of contemporary art and art theory and those working on the integration of art and theory/philosophy/psychology) but also the wider audience for contemporary art.

Redefining the outer boundaries of EU Law: the Zambrano, McCarthy and Dereci trilogy

In its three recent rulings in the cases of Zambrano, McCarthy, and Dereci, the Court appears to have been determined to redefine the external boundaries of EU law, in cases involving the family reunification rights of Union citizens.These three judgments can be read as an indication that for Article 20 TFEU to apply, there is no longer a requirement of a cross-border element on the facts of the case, and that it is sufficient if the contested national measure has the effect of ‘depriving citizens of the Union of the genuine enjoyment of the substance’ of their rights (the ‘Zambrano principle’).The cases can, at the same time, also be read as a confirmation that the free movement provisions do – still – require a cross-border element and, in particular, the exercise of inter-State movement, in order to apply. Though the result in these cases has not been entirely unexpected, especially in the aftermath of the Rottmann ruling, it is rather problematic in that, although it is obvious that the Court wishes to redraw the line dividing the national and EU spheres of competence, it does not make it entirely clear where this line now lies and leaves many essential questions unanswered, which will obviously require some time to be resolved. EU lawyers are consequently, once more, left with having to decipher as best as they can the real intentions of the Court in this new line of case-law, which has been further complicated by the fact that what the Court seems to have given with one hand in Zambrano (and before that in Rottmann), has taken it back to a large extent through its rulings in McCarthy and Dereci, which appear to confine the former two cases to their own exceptional facts.6 Moreover, the ‘reverse discrimination Pandora’s box’, the opening of which appears to have been the real target of these references, remains untouched: instead of providing a direct solution to this problem, the Court has chosen to – once again – broaden the scope of the Treaty provisions in order to include within it as many situations as possible and, thus, prevent the emergence of this type of differential treatment on a case-by-case basis.As will be explained, nonetheless, this is by no means an appropriate solution to the reverse discrimination conundrum.