P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Realistic mean field forward predictions for the integration of co-registered EEG/fMRI

Brain activity can be measured non-invasively with functional imaging techniques. Each pixel in such an image represents a neural mass of about 105 to 107 neurons. Mean field models (MFMs) approximate their activity by averaging out neural variability while retaining salient underlying features, like neurotransmitter kinetics. However, MFMs incorporating the regional variability, realistic geometry and connectivity of cortex have so far appeared intractable. This lack of biological realism has led to a focus on gross temporal features of the EEG. We address these impediments and showcase a "proof of principle" forward prediction of co-registered EEG/fMRI for a full-size human cortex in a realistic head model with anatomical connectivity, see figure 1. MFMs usually assume homogeneous neural masses, isotropic long-range connectivity and simplistic signal expression to allow rapid computation with partial differential equations. But these approximations are insufficient in particular for the high spatial resolution obtained with fMRI, since different cortical areas vary in their architectonic and dynamical properties, have complex connectivity, and can contribute non-trivially to the measured signal. Our code instead supports the local variation of model parameters and freely chosen connectivity for many thousand triangulation nodes spanning a cortical surface extracted from structural MRI. This allows the introduction of realistic anatomical and physiological parameters for cortical areas and their connectivity, including both intra- and inter-area connections. Proper cortical folding and conduction through a realistic head model is then added to obtain accurate signal expression for a comparison to experimental data. To showcase the synergy of these computational developments, we predict simultaneously EEG and fMRI BOLD responses by adding an established model for neurovascular coupling and convolving "Balloon-Windkessel" hemodynamics. We also incorporate regional connectivity extracted from the CoCoMac database [1]. Importantly, these extensions can be easily adapted according to future insights and data. Furthermore, while our own simulation is based on one specific MFM [2], the computational framework is general and can be applied to models favored by the user. Finally, we provide a brief outlook on improving the integration of multi-modal imaging data through iterative fits of a single underlying MFM in this realistic simulation framework.

A Lagrangian model of air-mass photochemistry and mixing using a trajectory ensemble: the Cambridge Tropospheric Trajectory model of Chemistry And Transport (CiTTyCAT) version 4.2

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

On the 'downward control' of extratropical diabatic circulations by eddy-induced mean zonal forces

The situation considered is that of a zonally symmetric model of the middle atmosphere subject to a given quasi-steady zonal force F̄, conceived to be the result of irreversible angular momentum transfer due to the upward propagation and breaking of Rossby and gravity waves together with any other dissipative eddy effects that may be relevant. The model's diabatic heating is assumed to have the qualitative character of a relaxation toward some radiatively determined temperature field. To the extent that the force F̄ may be regarded as given, and the extratropical angular momentum distribution is realistic, the extratropical diabatic mass flow across a given isentropic surface may be regarded as controlled exclusively by the F̄ distribution above that surface (implying control by the eddy dissipation above that surface and not, for instance, by the frequency of tropopause folding below). This “downward control” principle expresses a critical part of the dynamical chain of cause and effect governing the average rate at which photochemical products like ozone become available for folding into, or otherwise descending into, the extratropical troposphere. The dynamical facts expressed by the principle are also relevant, for instance, to understanding the seasonal-mean rate of upwelling of water vapor to the summer mesopause, and the interhemispheric differences in stratospheric tracer transport. The robustness of the principle is examined when F̄ is time-dependent. For a global-scale, zonally symmetric diabatic circulation with a Brewer-Dobson-like horizontal structure given by the second zonally symmetric Hough mode, with Rossby height HR = 13 km in an isothermal atmosphere with density scale height H = 7 km, the vertical partitioning of the unsteady part of the mass circulation caused by fluctuations in F̄ confined to a shallow layer LF̄ is always at least 84% downward. It is 90% downward when the force fluctuates sinusoidally on twice the radiative relaxation timescale and 95% if five times slower. The time-dependent adjustment when F̄ is changed suddenly is elucidated, extending the work of Dickinson (1968), when the atmosphere is unbounded above and below. Above the forcing, the adjustment is characterized by decay of the meridional mass circulation cell at a rate proportional to the radiative relaxation rate τr−1 divided by {1 + (4H2/HR2)}. This decay is related to the boundedness of the angular momentum that can be taken up by the finite mass of air above LF̄ without causing an ever-increasing departure from thermal wind balance. Below the forcing, the meridional mass circulation cell penetrates downward at a speed τr−1 HR2/H. For the second Hough mode, the time for downward penetration through one density scale height is about 6 days if the radiative relaxation time is 20 days, the latter being representative of the lower stratosphere. At any given altitude, a steady state is approached. The effect of a rigid lower boundary on the time-dependent adjustment is also considered. If a frictional planetary boundary layer is present then a steady state is ultimately approached everywhere, with the mass circulation extending downward from LF̄ and closing via the boundary layer. Satellite observations of temperature and ozone are used in conjunction with a radiative transfer scheme to estimate the altitudes from which the lower stratospheric diabatic vertical velocity is controlled by the effective F̄ in the real atmosphere. The data appear to indicate that about 80% of the effective control is usually exerted from below 40 km but with significant exceptions up to 70 km (in the high latitude southern hemispheric winter). The implications for numerical modelling of chemical transport are noted.

Expression of epitope-tagged LMW glutenin subunits in the starchy endosperm of transgenic wheat and their incorporation into glutenin polymers

The low-molecular-weight (LMW) glutenin subunits are components of the highly cross-linked glutenin polymers that confer viscoelastic properties to gluten and dough. They have both quantitative and qualitative effects on dough quality that may relate to differences in their ability to form the inter-chain disulphide bonds that stabilise the polymers. In order to determine the relationship between dough quality and the amounts and properties of the LMW subunits, we have transformed the pasta wheat cultivars Svevo and Ofanto with three genes encoding proteins, which differ in their numbers or positions of cysteine residues. The transgenes were delivered under control of the high-molecular-weight (HMW) subunit 1Dx5 gene promoter and terminator regions, and the encoded proteins were C-terminally tagged by the introduction of the c-myc epitope. Stable transformants were obtained with both cultivars, and the use of a specific antibody to the c-myc epitope tag allowed the transgene products to be readily detected in the complex mixture of LMW subunits. A range of transgene expression levels was observed. The addition of the epitope tag did not compromise the correct folding of the trangenic subunits and their incorporation into the glutenin polymers. Our results demonstrate that the ability to specifically epitope-tag LMW glutenin transgenes can greatly assist in the elucidation of their individual contributions to the functionality of the complex gluten system.

Multivalency in healable supramolecular polymers: the effect of supramolecular cross-link density on the mechanical properties and healing of noncovalent polymer networks

Polymers with the ability to heal themselves could provide access to materials with extended lifetimes in a wide range of applications such as surface coatings, automotive components and aerospace composites. Here we describe the synthesis and characterisation of two novel, stimuli-responsive, supramolecular polymer blends based on π-electron-rich pyrenyl residues and π-electron-deficient, chain-folding aromatic diimides that interact through complementary π–π stacking interactions. Different degrees of supramolecular “cross-linking” were achieved by use of divalent or trivalent poly(ethylene glycol)-based polymers featuring pyrenyl end-groups, blended with a known diimide–ether copolymer. The mechanical properties of the resulting polymer blends revealed that higher degrees of supramolecular “cross-link density” yield materials with enhanced mechanical properties, such as increased tensile modulus, modulus of toughness, elasticity and yield point. After a number of break/heal cycles, these materials were found to retain the characteristics of the pristine polymer blend, and this new approach thus offers a simple route to mechanically robust yet healable materials.

Folding of graphene slit like pore walls—a simple method of improving CO2 separation from mixtures with CH4 or N2

We report for the first time a detailed procedure for creating a simulation model of energetically stable, folded graphene-like pores and simulation results of CO2/CH4 and CO2/N2 separation using these structures. We show that folding of graphene structures is a very promising method to improve the separation of CO2 from mixtures with CH4 and N2. The separation properties of the analyzed materials are compared with carbon nanotubes having similar diameters or S/V ratio. The presented results have potential importance in the field of CO2 capture and sequestration.

In silico identification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis

Background Dermatosparaxis (Ehlers–Danlos syndrome in humans) is characterized by extreme fragility of the skin. It is due to the lack of mature collagen caused by a failure in the enzymatic processing of procollagen I. We investigated the condition in a commercial sheep flock. Hypothesis/Objectives Mutations in the ADAM metallopeptidase with thrombospondin type 1 motif, 2 (ADAMTS2) locus, are involved in the development of dermatosparaxis in humans, cattle and the dorper sheep breed; consequently, this locus was investigated in the flock. Animals A single affected lamb, its dam, the dam of a second affected lamb and the rams in the flock were studied. Methods DNA was purified from blood, PCR primers were used to detect parts of the ADAMS2 gene and nucleotide sequencing was performed using Sanger's procedure. Skin samples were examined using standard histology procedures. Results A missense mutation was identified in the catalytic domain of ADAMTS2. The mutation is predicted to cause the substitution in the mature ADAMTS2 of a valine molecule by a methionine molecule (V15M) affecting the catalytic domain of the enzyme. Both the ‘sorting intolerant from tolerant’ (SIFT) and the PolyPhen-2 methodologies predicted a damaging effect for the mutation. Three-dimensional modelling suggested that this mutation may alter the stability of the protein folding or distort the structure, causing the protein to malfunction. Conclusions and clinical importance Detection of the mutation responsible for the pathology allowed us to remove the heterozygote ram, thus preventing additional cases in the flock.

Molecular design of a discrete chain-folding polyimide for controlled inkjet deposition of supramolecular polymers

A supramolecular polymer based upon two complementary polymer components is formed by sequential deposition from solution in THF, using a piezoelectric drop-on-demand inkjet printer. Highly efficient cycloaddition or ‘click’ chemistry afforded a well-defined poly(ethylene glycol) featuring chain-folding diimide end groups, which possesses greatly enhanced solubility in THF relative to earlier materials featuring random diimide sequences. Blending the new polyimide with a complementary poly(ethylene glycol) system bearing pyrene end groups (which bind to the chain-folding diimide units) overcomes the limited solubility encountered previously with chain-folding polyimides in inkjet printing applications. The solution state properties of the resulting polymer blend were assessed via viscometry to confirm the presence of a supramolecular polymer before depositing the two electronically complementary polymers by inkjet printing techniques. The novel materials so produced offer an insight into ways of controlling the properties of printed materials through tuning the structure of the polymer at the (supra)molecular level.

The proteome of the infectious bronchitis virus Beau-R Virion

Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavirus IBV. It was thought that coronavirus virions were composed of three major viral structural proteins, until investigations of other coronaviruses showed that coronavirus virions also include viral non-structural and group specific proteins as well as host cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation and analysed by mass spectrometry proteomic. Analysis of three preparations of purified IBV yielded the three expected structural proteins plus thirty-five additional virion-associated host proteins. Virion-associated host proteins had a diverse range of functional attributions, being involved in cytoskeleton formation, RNA binding and protein folding pathways. Some of these proteins were unique to this study, whilst others were found to be orthologous to proteins identified in SARS-CoV virions, and also virions from a number of other RNA and DNA viruses. Together these results demonstrate that coronaviruses have the capacity to incorporate a substantial variety of host protein, which may have implications for the disease process.

Probing the (6,7)Li nucleon densities through a new break-up process approach

In this work we present a double folding optical model analysis of new near-barrier quasi-elastic experimental data for the (6,7)Li + (120)Sn systems. From the analysis, it was possible to confirm the ground-state nucleon densities assumed for the weakly bound (6,7)Li isotopes. The apparent discrepancies between the experimental densities and those based on Dirac-Hartree-Fock Bogoliubov (DHB) calculations were removed. A new approach that simulates the projectile break-up and a positive polarization from couplings of (6,7)Li bound states with the continuum was considered in the reaction mechanism. (C) 2010 Elsevier B.V. All rights reserved.

Understanding fusion suppression and enhancement in the (18)O+(58,60,64)Ni systems

Realistic coupled-channel calculation results for the (18)[O] + (58,60,64)Ni systems in the bombarding energy range 34.5 <= E(Lab) <= 6-5 MeV are presented. The overall agreement with existing experimental data is quite good. Our calculations predict an unexpected fusion suppression for above-barrier energies, with an important contribution of the two neutron ((18)O, (16)O) transfer channel couplings. The sub-barrier fusion enhancement and the above barrier suppression, predicted by the calculations, are consistent with the nuclear structure of the Ni region. Comparisons with recently reported similar effects in reactions induced by the (6)He projectile are discussed. (C) 2009 Elsevier B.V. All rights reserved.

Study of (9)Be+(12)C elastic scattering at energies near the Coulomb barrier

In this work, angular distribution measurements for the elastic channel were performed for the (9)Be + (12)C reaction at the energies E(Lab) = 13.0, 14.5, 17.3, 19.0 and 21.0 MeV, near the Coulomb barrier. The data have been analyzed in the framework of the double folding Sao Paulo potential. The experimental elastic scattering angular distributions were well described by the optical potential at forward angles for all measured energies. However, for the three highest energies, an enhancement was observed for intermediate and backward angles. This can be explained by the elastic transfer mechanism. (C) 2011 Elsevier B.V. All rights reserved.

Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability

The structural stability of a peroxidase, a dimeric protein from royal palm tree (Roystonea regia) leaves, has been characterized by high-sensitivity differential scanning calorimetry, circular dichroism, steady-state tryptophan fluorescence and analytical ultracentifugation under different solvent conditions. It is shown that the thermal and chemical (using guanidine hydrochloride (Gdn-HCl)) folding/unfolding of royal palm tree peroxidase (RPTP) at pH 7 is a reversible process involving a highly cooperative transition between the folded dimer and unfolded monomers, with a free stabilization energy of about 23 kcal per mol of monomer at 25 degrees C. The structural stability of RPTP is pH-dependent. At pH 3, where ion pairs have disappeared due to protonation, the thermally induced denaturation of RPTP is irreversible and strongly dependent upon the scan rate, suggesting that this process is under kinetic control. Moreover, thermally induced transitions at this pH value are dependent on the protein concentration, allowing it to be concluded that in solution RPTP behaves as dimer, which undergoes thermal denaturation coupled with dissociation. Analysis of the kinetic parameters of RPTP denaturation at pH 3 was accomplished on the basis of the simple kinetic scheme N ->(k) D, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state, and thermodynamic information was obtained by extrapolation of the kinetic transition parameters to an infinite heating rate. Obtained in this way, the value of RPTP stability at 25 degrees C is ca. 8 kcal per mole of monomer lower than at pH 7. In all probability, this quantity reflects the contribution of ion pair interactions to the structural stability of RPTP. From a comparison of the stability of RPTP with other plant peroxidases it is proposed that one of the main factors responsible for the unusually high stability of RPTP which enhances its potential use for biotechnological purposes, is its dimerization. (c) 2008 Elsevier Masson SAS. All rights reserved.

Constraining the age of the iporanga formation with SHRIMP U-Pb zircon: Implications for possible ediacaran glaciation in the Ribeira Belt, SE Brazil

The Ribeira belt in SE Brazil is a Neoproterozoic to Early Palaeozoic orogen, whose architecture and history is not yet fully understood. The depositional age of many of the sedimentary sequences in the Ribeira Belt remains unconstrained, and with debate concerning their depositional environment and tectonic setting. In this paper we present SHRIMP zircon U/Pb age constraints for one such problematic unit in the Ribeira Belt the lporanga Formation - and discuss the significance of this age with regards to the timing of Neoproterozoic glacial events in southeast Brazil. Using a felsic volcanic unit immediately under the lporanga Formation and granite cobbles from breccias in its basal parts a reconnaissance SHRIMP U/Pb zircon maximum depositional age of 580 Ma is assigned for the base of this unit. This age is marginally younger than the 625605 Ma ages for intrusions into the Lajeado and Ribeira subgroups, with which the lporanga Formation is in tectonic contact. This indicates that the Lajeado and Ribeira subgroups are not stratigraphically equivalent to the lporanga Formation, as thought previously by some workers. The maximum depositional age of 580 Ma also places a maximum time constraint on the tectonic juxtaposition of the lporanga Formation with other supracrustal units, and on the greenschist facies metamorphism and isoclinal folding that affected it. The potential glacial origin for the lporanga Formation, if correct, would place it in the late Ediacaran - provisionally equivalent to the Gaskiers glaciation. (c) 2007 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.