Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Pipelining considerations for an FPGA case

This paper presents a semi-synchronous pipeline scheme, here referred as single-pulse pipeline, to the problem of mapping pipelined circuits to a Field Programmable Gate Array (FPGA). Area and timing considerations are given for a general case and later applied to a systolic circuit as illustration. The single-pulse pipeline can manage asynchronous worst-case data completion and it is evaluated against two chosen asynchronous pipelining: a four-phase bundle-data pipeline and a doubly-latched asynchronous pipeline. The semi-synchronous pipeline proposal takes less FPGA area and operates faster than the two selected fully-asynchronous schemes for an FPGA case.

The Ferritin-like superfamily: evolution of the biological iron storeman from a rubrerythrin-like ancestor

Background: The Ferritins are part of the extensive ‘Ferritin-like superfamily’ which have diverse functions but are linked by the presence of a common four-helical bundle domain. The role performed by Ferritins as the cellular repository of excess iron is unique. In many ways Ferritins act as tiny organelles in their ability to secrete iron away from the delicate machinery of the cell, and then to release it again in a controlled fashion avoiding toxicity. The Ferritins are ancient proteins, being common in all three domains of life. This ubiquity reflects the key contribution that Ferritins provide in achieving iron homeostasis. Scope of the review: This review compares the features of the different Ferritins and considers how they, and other members of the Ferritin-like superfamily, have evolved. It also considers relevant features of the eleven other known families within the Ferritin-like superfamily, particularly the highly diverse rubrerythrins. Major conclusions: The Ferritins have travelled a considerable evolutionary journey, being derived from far more simplistic rubrerythrin-like molecules which play roles in defence against toxic oxygen species. The forces of evolution have moulded such molecules into three distinct types of iron storing (or detoxifying) protein: the classical and universal 24-meric ferritins; the haem-containing 24-meric bacterioferritins of prokaryotes; and the prokaryotic 12-meric Dps proteins. These three Ferritin types are similar, but also possess unique properties that distinguish them and enable then to achieve their specific physiological purposes. General significance: A wide range of biological functions have evolved from a relatively simple structural unit.

Food-chain transfer of cadmium and zinc from contaminated Urtica dioica to Helix aspersa and Lumbricus terrestris

The present study examines the potential of Urtica dioica as an ecologically relevant species for use in ecotoxicological testing. It is prevalent in degraded ecosystems and is a food source for invertebrates. Urtica dioica grown in hydroponic solutions containing from less than 0.003 to 5.7 mg Cd/L or from 0.02 to 41.9 mg Zn/L accumulated metals resulting in leaf tissue concentrations in the range of 0.10 to 24.9 mg Cd/kg or 22.5 to 2,772.0 mg Zn/kg. No toxicological effects were apparent except at the highest concentrations tested, suggesting that this species may be an important pathway for transfer of metals to primary plant consumers. Helix aspersa and Lumbricus terrestris were fed the Cd- and Zn-rich leaves of U. dioica for six and four weeks, respectively. Cadmium and Zn body load increased with increasing metal concentration in the leaves (p < 0.001). Ratios of invertebrate metal concentration to leaf metal concentration were in the range of 1:0.03 to 1:1.4 for Cd and 1:0.2 to 1:2.8 for Zn in H. aspersa and 1:0.002 to 1:3.9 for Cd and 1:0.2 to 1:8.8 for Zn in L. terrestris. Helix aspersa Cd and Zn tissue concentrations (15.5 and 1,220.2 mg/kg, respectively) were approximately threefold those in L. terrestris when both species were fed nettle leaves with concentrations of approximately 23 mg Cd/ kg and 3,400 mg Zn/kg. Models demonstrate that L. terrestris Cd tissue concentrations (r(2) = 0.74, p < 0.001) and H. aspersa Zn tissue concentrations (r(2) = 0.69, p < 0.001) can be estimated from concentrations of Cd and Zn within the leaves of U. dioica and suggest that reasonably reproducible results can be obtained using these species for ecotoxicological testing.

Overlapping double turn conformations adopted by tetrapeptides containing non-coded alpha-Amino Isobutyric Acid (AIB) and formation of tape-like structures through supramolecular helix mediated self-assembly

Single crystal X-ray diffraction studies and solvent dependent H-1 NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L- amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4 -> 1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning electron microscopic (FE-SEM) images of the tetrapeptides in the solid state reveal that they can form flat tape-like structures. The results establish that synthetic Aib containing supramolecular helices can form highly ordered self-aggregated amyloid plaque like human amylin.

A unique example of structural and magnetic diversity in four interconvertible copper(II)−azide complexes with the same Schiff base ligand: a monomer, a dimer, a chain, and a layer

Four new Cu(II)-azido complexes of formula [CuL(N-3)] (1), [CuL(N-3)](2) (2), [Cu7L2(N-3)(12)](n) (3), and [Cu2L(dmen)-(N-3)(3)](n) (4) (dmen = N,N-dimethylethylenediamine) have been synthesized using the same tridentate Schiff base ligand HL (2-[1-(2-dimethylaminoethylimino)ethyl]phenol, the condensation product of dmen and 2-hydroxyacetophenone). The four compounds have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. Complex 1 is mononuclear, whereas 2 is a single mu-1,1 azido-bridged dinuclear compound. The polymeric compound 3 possesses a 2D structure in which the Cu(II) ions are linked by phenoxo oxygen atoms and two different azide bridges (mu-1,1 and mu-1,1,3). The structure of complex 4 is a double helix in which two mu-1,3-azido-bridged alternating one-dimensional helical chains of CuL(N-3) and Cu(dmen)(N-3)(2) are joined together by weak mu-1,1 azido bridges and H-bonds. The complexes interconvert in solution and can be obtained in pure form by carefully controlling the conditions. The magnetic properties of compounds 1 and 2 show the presence of very weak antiferromagnetic exchange interactions mediated by a ligand pi overlap (J = -1.77) and by an asymmetric 1,1-N-3 bridge (J = -1.97 cm(-1)), respectively. Compound 3 presents, from the magnetic point of view, a decorated chain structure with both ferro- and antiferromagnetic interactions. Compound 4 is an alternating helicoidal chain with two weak antiferromagnetic exchange interactions (J -1.35 and -2.64 cm(-1)).

Weak constraints in four-dimensional variational data assimilation

The formulation of four-dimensional variational data assimilation allows the incorporation of constraints into the cost function which need only be weakly satisfied. In this paper we investigate the value of imposing conservation properties as weak constraints. Using the example of the two-body problem of celestial mechanics we compare weak constraints based on conservation laws with a constraint on the background state.We show how the imposition of conservation-based weak constraints changes the nature of the gradient equation. Assimilation experiments demonstrate how this can add extra information to the assimilation process, even when the underlying numerical model is conserving.

Four-dimensional variational assimilation of ozone profiles from the Microwave Limb Sounder on the Aura satellite

Ozone profiles from the Microwave Limb Sounder (MLS) onboard the Aura satellite of the NASA's Earth Observing System (EOS) were experimentally added to the European Centre for Medium-range Weather Forecasts (ECMWF) four-dimensional variational (4D-var) data assimilation system of version CY30R1, in which total ozone columns from Scanning Imaging Absorption Spectrometer for Atmospheric CHartographY (SCIAMACHY) onboard the Envisat satellite and partial profiles from the Solar Backscatter Ultraviolet (SBUV/2) instrument onboard the NOAA-16 satellite have been operationally assimilated. As shown by results for the autumn of 2005, additional constraints from MLS data significantly improved the agreement of the analyzed ozone fields with independent observations throughout most of the stratosphere, owing to the daily near-global coverage and good vertical resolution of MLS observations. The largest impacts were seen in the middle and lower stratosphere, where model deficiencies could not be effectively corrected by the operational observations without the additional information on the ozone vertical distribution provided by MLS. Even in the upper stratosphere, where ozone concentrations are mainly determined by rapid chemical processes, dense and vertically resolved MLS data helped reduce the biases related to model deficiencies. These improvements resulted in a more realistic and consistent description of spatial and temporal variations in stratospheric ozone, as demonstrated by cases in the dynamically and chemically active regions. However, combined assimilation of the often discrepant ozone observations might lead to underestimation of tropospheric ozone. In addition, model deficiencies induced large biases in the upper stratosphere in the medium-range (5-day) ozone forecasts.

The four major N- and C-terminal splice variants of the excitatory amino acid transporter GLT-1 form cell surface homomeric and heteromeric assemblies

The L-glutamate transporter GLT-1 is an abundant CNS membrane protein of the excitatory amino acid transporter (EAAT) family which controls extracellular L-glutamate levels and is important in limiting excitotoxic neuronal death. Using RT-PCR, we have determined that four mRNAs encoding GLT-1 exist in mouse brain, with the potential to encode four GLT-1 isoforms that differ in their N- and C-termini. We expressed all four isoforms (termed MAST-KREK, MPK-KREK, MAST-DIETCI and MPK-DIETCI according to amino acid sequence) in a range of cell lines and primary astrocytes and show that each isoform can reach the cell surface. In transfected HEK-293 or COS-7 cells, all four isoforms support high-affinity sodium-dependent L-glutamate uptake with identical pharmacological and kinetic properties. Inserting a viral epitope (V5, HA or FLAG) into the second extracellular domain of each isoform allowed co-immunoprecipitation and tr-FRET studies using transfected HEK-293 cells. Here we show for the first time that each of the four isoforms are able to combine to form homomeric and heteromeric assemblies, each of which are expressed at the cell surface of primary astrocytes. After activation of protein kinase C by phorbol ester, V5-tagged GLT-1 is rapidly removed from the cell surface of HEK-293 cells and degraded. This study provides direct biochemical evidence for oligomeric assembly of GLT-1 and reports the development of novel tools to provide insight into the trafficking of GLT-1.

Preparation of consistent soil data sets for modelling purposes: Secondary SOTER data for four case study areas

The common GIS-based approach to regional analyses of soil organic carbon (SOC) stocks and changes is to define geographic layers for which unique sets of driving variables are derived, which include land use, climate, and soils. These GIS layers, with their associated attribute data, can then be fed into a range of empirical and dynamic models. Common methodologies for collating and formatting regional data sets on land use, climate, and soils were adopted for the project Assessment of Soil Organic Carbon Stocks and Changes at National Scale (GEFSOC). This permitted the development of a uniform protocol for handling the various input for the dynamic GEFSOC Modelling System. Consistent soil data sets for Amazon-Brazil, the Indo-Gangetic Plains (IGP) of India, Jordan and Kenya, the case study areas considered in the GEFSOC project, were prepared using methodologies developed for the World Soils and Terrain Database (SOTER). The approach involved three main stages: (1) compiling new soil geographic and attribute data in SOTER format; (2) using expert estimates and common sense to fill selected gaps in the measured or primary data; (3) using a scheme of taxonomy-based pedotransfer rules and expert-rules to derive soil parameter estimates for similar soil units with missing soil analytical data. The most appropriate approach varied from country to country, depending largely on the overall accessibility and quality of the primary soil data available in the case study areas. The secondary SOTER data sets discussed here are appropriate for a wide range of environmental applications at national scale. These include agro-ecological zoning, land evaluation, modelling of soil C stocks and changes, and studies of soil vulnerability to pollution. Estimates of national-scale stocks of SOC, calculated using SOTER methods, are presented as a first example of database application. Independent estimates of SOC stocks are needed to evaluate the outcome of the GEFSOC Modelling System for current conditions of land use and climate. (C) 2007 Elsevier B.V. All rights reserved.

Assessment of the effect of time and temperature on the availability of residual phosphate in a glasshouse study of four soils using the Olsen method

The Olsen method is an indicator of plant-available phosphorus (P). The effect of time and temperature on residual phosphate in soils was measured using the Olsen method in a pot experiment. Four soils were investigated: two from Pakistan and one each from England (calcareous) and Colombia (acidic). Two levels of residual phosphate were developed in each soil after addition of phosphate by incubation at either 10degreesC or 45degreesC. The amount of phosphate added was based on the P maximum of each soil, calculated using the Langmuir equation. Rvegrass was used as the test crop. The pooled data for the four soils incubated at 10degreesC showed good correlation between Olsen P and dry matter yield or P uptake (r(2) = 0.85 and 0.77, respectively), whereas at 45 degreesC, each soil had its own relationship and pooled data did not show correlation of Olsen P with dry matter yield or P uptake. When the data at both temperatures were pooled, Olsen P was a good indicator of yield and uptake for the English soil. For the Pakistani soils, Olsen P after 45 degreesC treatment was an underestimate relative to the 10 degreesC data and for the Colombian soil it was an overestimate. The reasons for these differences need to be explored further before high temperature incubation can be used to simulate long-term changes in the field.

Degradation and plant uptake of nonylphenol (NP) and nonylphenol-12-ethoxylate (NP12EO) in four contrasting agricultural soils

Nonylphenol polyethoxylates (NPEOs) are surfactants found ubiquitously in the environment due to widespread industrial and domestic use. Biodegradation of NPEOs produces nonylphenol (NP), an endocrine disruptor. Sewage sludge application introduces NPEOs and NP into soils, potentially leading to accumulation in soils and crops. We examined degradation of NP and nonyl phenol-12-ethoxylate (NP12EO) in four soils. NP12EO degraded rapidly (initial half time 0.3-5 days). Concentrations became undetectable within 70-90 days, with a small increase in NP concentrations after 30 days. NP initially degraded quickly (mean half time 11.5 days), but in three soils a recalcitrant fraction of 26-35% remained: the non-degrading fraction may consist of branched isomers, resistant to biodegradation. Uptake of NP by bean plants was also examined. Mean bioconcentration factors for shoots and seeds were 0.71 and 0.58, respectively. Removal of NP from the soil by plant uptake was negligible (0.01-0.02% of initial NP). Root concentrations were substantially higher than shoot and seed concentrations. (C) 2008 Elsevier Ltd. All rights reserved.

Estimating uncertainty in terrestrial critical loads and their exceedances at four sites in the UK

Critical loads are the basis for policies controlling emissions of acidic substances in Europe and elsewhere. They are assessed by several elaborate and ingenious models, each of which requires many parameters, and have to be applied on a spatially-distributed basis. Often the values of the input parameters are poorly known, calling into question the validity of the calculated critical loads. This paper attempts to quantify the uncertainty in the critical loads due to this "parameter uncertainty", using examples from the UK. Models used for calculating critical loads for deposition of acidity and nitrogen in forest and heathland ecosystems were tested at four contrasting sites. Uncertainty was assessed by Monte Carlo methods. Each input parameter or variable was assigned a value, range and distribution in an objective a fashion as possible. Each model was run 5000 times at each site using parameters sampled from these input distributions. Output distributions of various critical load parameters were calculated. The results were surprising. Confidence limits of the calculated critical loads were typically considerably narrower than those of most of the input parameters. This may be due to a "compensation of errors" mechanism. The range of possible critical load values at a given site is however rather wide, and the tails of the distributions are typically long. The deposition reductions required for a high level of confidence that the critical load is not exceeded are thus likely to be large. The implication for pollutant regulation is that requiring a high probability of non-exceedance is likely to carry high costs. The relative contribution of the input variables to critical load uncertainty varied from site to site: any input variable could be important, and thus it was not possible to identify variables as likely targets for research into narrowing uncertainties. Sites where a number of good measurements of input parameters were available had lower uncertainties, so use of in situ measurement could be a valuable way of reducing critical load uncertainty at particularly valuable or disputed sites. From a restricted number of samples, uncertainties in heathland critical loads appear comparable to those of coniferous forest, and nutrient nitrogen critical loads to those of acidity. It was important to include correlations between input variables in the Monte Carlo analysis, but choice of statistical distribution type was of lesser importance. Overall, the analysis provided objective support for the continued use of critical loads in policy development. (c) 2007 Elsevier B.V. All rights reserved.