Catalysis by Modified Pillared Clays and Porous Clay Heterostructures

In this venture three distinct class of catalysts such as, pillared clays and transition metal loaded pillared clays , porous clay heterostructures and their transition metal loaded analogues and DTP supported on porous clay heterostructures etc. were prepared and characterized by various physico chemical methods. The catalytic activities of prepared catalysts were comparatively evaluated for the industrially important alkylation, acetalization and oxidation reactions.The general conclusions drawn from the present investigation are  Zirconium, iron - aluminium pillared clays were synthesized by ion exchange method and zirconium-silicon porous heterostructures were Summary and conclusions 259 prepared by intergallery template method. Transition metals were loaded in PILCs and PCHs by wet impregnation method.  Textural and acidic properties of the clays were modified by pillaring and post pillaring modifications.  The shift in 2θ value to lower range and increase in d (001) spacing indicate the success of pillaring process.  Surface area, pore volume, average pore size etc. increased dramatically as a result of pillaring process.  Porous clay heterostructures have higher surface area, pore volume, average pore diameter and narrow pore size distribution than that of pillared clays.  The IR spectrum of PILCs and PCHs are in accordance with literature without much variation compared to parent montmorillonite which indicate that basic clay structure is retained even after modification.  The silicon NMR of PCHs materials have intense peaks corresponding to Q4 environment which indicate that mesoporous silica is incorporated between clay layers.  Thermo gravimetric analysis showed that thermal stability is improved after the pillaring process. PCH materials have higher thermal stability than PILCs.  In metal loaded pillared clays, up to 5% metal species were uniformly dispersed (with the exception of Ni) as evident from XRD and TPR analysis. Chapter 9 260  Impregnation of transition metals in PILCs and PCHs enhanced acidity of catalysts as evident from TPD of ammonia and cumene cracking reactions.  For porous clay heterostructures the acidic sites have major contribution from weak and medium acid sites which can be related to the Bronsted sites as evident from TPD of ammonia.  Pillared clays got more Lewis acidity than PCHs as inferred from α- methyl styrene selectivity in cumene cracking reaction.  SEM images show that layer structure is preserved even after modification. Worm hole like morphology is observed in TEM image of PCHs materials  In ZrSiPCHS, Zr exists as Zr 4+ and is incorporated to silica pillars in the intergallary of clay layers as evident from XPS analysis.  In copper loaded zirconium pillared clays, copper exists as isolated species with +2 oxidation state at lower loading. At higher loading, Cu exists as clusters as evident from reduction peak at higher temperatures in TPR.  In vanadium incorporated PILCs and PCHs, vanadium exist as isolated V5+ in tetrahedral coordination which is confirmed from TPR and UVVis DRS analysis.  In cobalt loaded PCHs, cobalt exists as CoO with 2+ oxidation state as confirmed from XPS.  Cerium incorporated iron aluminium pillared clay was found to be the best catalyst for the hydroxylation of phenol in aqueous media due to the additional surface area provided by ceria mesopores and its redox properties. Summary and conclusions 261  Cobalt loaded zirconium porous clay heterostructures were found to be promising catalyst for the tertiary butylation of phenol due to higher surface area and acidic properties.  Copper loaded pillared clays were found to be good catalyst for the direct hydroxylation of benzene to phenol.  Vanadium loaded PCHs catalysts were found to be efficient catalysts for oxidation of benzyl alcohol.  DTP was firmly fixed on the mesoporous channels of PCHs by Direct method and functionalization method.  DTP supported PCHs catalyst were found to be good catalyst for acetalization of cyclohexanone with more than 90% conversion.

Study on period search methods of variable stars: Application to ASAS and CRTS databases

Study on variable stars is an important topic of modern astrophysics. After the invention of powerful telescopes and high resolving powered CCD’s, the variable star data is accumulating in the order of peta-bytes. The huge amount of data need lot of automated methods as well as human experts. This thesis is devoted to the data analysis on variable star’s astronomical time series data and hence belong to the inter-disciplinary topic, Astrostatistics. For an observer on earth, stars that have a change in apparent brightness over time are called variable stars. The variation in brightness may be regular (periodic), quasi periodic (semi-periodic) or irregular manner (aperiodic) and are caused by various reasons. In some cases, the variation is due to some internal thermo-nuclear processes, which are generally known as intrinsic vari- ables and in some other cases, it is due to some external processes, like eclipse or rotation, which are known as extrinsic variables. Intrinsic variables can be further grouped into pulsating variables, eruptive variables and flare stars. Extrinsic variables are grouped into eclipsing binary stars and chromospheri- cal stars. Pulsating variables can again classified into Cepheid, RR Lyrae, RV Tauri, Delta Scuti, Mira etc. The eruptive or cataclysmic variables are novae, supernovae, etc., which rarely occurs and are not periodic phenomena. Most of the other variations are periodic in nature. Variable stars can be observed through many ways such as photometry, spectrophotometry and spectroscopy. The sequence of photometric observa- xiv tions on variable stars produces time series data, which contains time, magni- tude and error. The plot between variable star’s apparent magnitude and time are known as light curve. If the time series data is folded on a period, the plot between apparent magnitude and phase is known as phased light curve. The unique shape of phased light curve is a characteristic of each type of variable star. One way to identify the type of variable star and to classify them is by visually looking at the phased light curve by an expert. For last several years, automated algorithms are used to classify a group of variable stars, with the help of computers. Research on variable stars can be divided into different stages like observa- tion, data reduction, data analysis, modeling and classification. The modeling on variable stars helps to determine the short-term and long-term behaviour and to construct theoretical models (for eg:- Wilson-Devinney model for eclips- ing binaries) and to derive stellar properties like mass, radius, luminosity, tem- perature, internal and external structure, chemical composition and evolution. The classification requires the determination of the basic parameters like pe- riod, amplitude and phase and also some other derived parameters. Out of these, period is the most important parameter since the wrong periods can lead to sparse light curves and misleading information. Time series analysis is a method of applying mathematical and statistical tests to data, to quantify the variation, understand the nature of time-varying phenomena, to gain physical understanding of the system and to predict future behavior of the system. Astronomical time series usually suffer from unevenly spaced time instants, varying error conditions and possibility of big gaps. This is due to daily varying daylight and the weather conditions for ground based observations and observations from space may suffer from the impact of cosmic ray particles. Many large scale astronomical surveys such as MACHO, OGLE, EROS, xv ROTSE, PLANET, Hipparcos, MISAO, NSVS, ASAS, Pan-STARRS, Ke- pler,ESA, Gaia, LSST, CRTS provide variable star’s time series data, even though their primary intention is not variable star observation. Center for Astrostatistics, Pennsylvania State University is established to help the astro- nomical community with the aid of statistical tools for harvesting and analysing archival data. Most of these surveys releases the data to the public for further analysis. There exist many period search algorithms through astronomical time se- ries analysis, which can be classified into parametric (assume some underlying distribution for data) and non-parametric (do not assume any statistical model like Gaussian etc.,) methods. Many of the parametric methods are based on variations of discrete Fourier transforms like Generalised Lomb-Scargle peri- odogram (GLSP) by Zechmeister(2009), Significant Spectrum (SigSpec) by Reegen(2007) etc. Non-parametric methods include Phase Dispersion Minimi- sation (PDM) by Stellingwerf(1978) and Cubic spline method by Akerlof(1994) etc. Even though most of the methods can be brought under automation, any of the method stated above could not fully recover the true periods. The wrong detection of period can be due to several reasons such as power leakage to other frequencies which is due to finite total interval, finite sampling interval and finite amount of data. Another problem is aliasing, which is due to the influence of regular sampling. Also spurious periods appear due to long gaps and power flow to harmonic frequencies is an inherent problem of Fourier methods. Hence obtaining the exact period of variable star from it’s time series data is still a difficult problem, in case of huge databases, when subjected to automation. As Matthew Templeton, AAVSO, states “Variable star data analysis is not always straightforward; large-scale, automated analysis design is non-trivial”. Derekas et al. 2007, Deb et.al. 2010 states “The processing of xvi huge amount of data in these databases is quite challenging, even when looking at seemingly small issues such as period determination and classification”. It will be beneficial for the variable star astronomical community, if basic parameters, such as period, amplitude and phase are obtained more accurately, when huge time series databases are subjected to automation. In the present thesis work, the theories of four popular period search methods are studied, the strength and weakness of these methods are evaluated by applying it on two survey databases and finally a modified form of cubic spline method is intro- duced to confirm the exact period of variable star. For the classification of new variable stars discovered and entering them in the “General Catalogue of Vari- able Stars” or other databases like “Variable Star Index“, the characteristics of the variability has to be quantified in term of variable star parameters.

Microbial use of organic substrates and maize growth, especially in saline and alkaline soils of Pakistani Punjab

This thesis consists of 4 main parts: (1) impact of growing maize on the decomposition of incorporated fresh alfalfa residues, (2) relationships between soil biological and other soil properties in saline and alkaline arable soils from the Pakistani Punjab, (3) decomposition of compost and plant residues in Pakistani soils along a gradient in salinity, and (4) interactions of compost and triple superphosphate on the growth of maize in a saline Pakistani soil. These 4 chapters are framed by a General Introduction and a Conclusions section. (1) In the first study, the effects of growing maize plants on the microbial decomposition of freshly chopped alfalfa residues was investigated in a 90-day pot experiment using a sandy arable soil. Assuming that the addition of alfalfa residues did not affect the decomposition of native soil organic matter, only 27% of the alfalfa residues were found as CO2. This suggests that a considerable part of alfalfa-C remained undecomposed in the soil. However, only 6% of the alfalfa residues could be recovered as plant remains in treatment with solely alfalfa residues. Based on d13C values, it was calculated that plant remains in treatment maize + alfalfa residues contained 14.7% alfalfa residues and 85.3% maize root remains. This means 60% more alfalfa-C was recovered in this treatment. (2) In the second study, the interactions between soil physical, soil chemical and soil biological properties were analysed in 30 Pakistani soils from alkaline and saline arable sites differing strongly in salinisation and in soil pH. The soil biological properties were differentiated into indices for microbial activity, microbial biomass, and community structure with the aim of assessing their potential as soil fertility indices. (3) In the third study, 3 organic amendments (compost, maize straw and pea straw) were added to 5 Pakistani soils from a gradient in salinity. Although salinity has depressive effects on microbial biomass C, biomass N, biomass P, and ergosterol, the clear gradient according to the soil salt concentration was not reflected by the soil microbial properties. The addition of the 3 organic amendments always increased the contents of the microbial indices analysed. The amendment-induced increase was especially strong for microbial biomass P and reflected the total P content of the added substrates. (4) The fourth study was greenhouse pot experiment with different combinations of compost and triple superphosphate amendments to investigate the interactions between plant growth, microbial biomass formation and compost decomposition in a strongly saline Pakistani arable soil in comparison to a non-saline German arable soil. The Pakistani soil had a 2 times lower content of ergosterol, a 4 times lower contents of microbial biomass C, biomass N and biomass P, but nearly a 20 times lower content of NaHCO3 extractable P. The addition of 1% compost always had positive effects on the microbial properties and also on the content of NaHCO3 extractable P. The addition of superphosphate induced a strong and similar absolute increase in microbial biomass P in both soils.

Facilitating folding of outer membrane proteins, roles of the periplasmic chaperone Skp and the outer membrane lipoprotein BamD

This thesis describes several important advancements in the understanding of the assembly of outer membrane proteins of Gram-negative bacteria like Escherichia coli. A first study was performed to identify binding regions in the trimeric chaperone Skp for outer membrane proteins. Skp is known to facilitate the passage of unfolded outer membrane proteins (OMPs) through the periplasm to the outer membrane (OM). A gene construct named “synthetic chaperone protein (scp)” gene was used to express a fusion protein (Scp) into the cytoplasm of E. coli. The scp gene was used as a template to design mutants of Scp suitable for structural and functional studies using site-directed spectroscopy. Fluorescence resonance energy transfer (FRET) was used to identify distances in Skp-OmpA complexes that separate regions in Scp and in outer membrane protein A (OmpA) from E. coli. For this study, single cysteine (Cys) mutants and single Cys - single tryptophan (Trp) double mutants of Scp were prepared. For FRET experiments, the cysteines were labeled with the tryptophan fluorescence energy acceptor IAEDANS. Single Trp mutants of OmpA were used as fluorescence energy donors. In the second part of this thesis, the function of BamD and the structure of BamD-Scp complexes were examined. BamD is an essential component of the β-barrel assembly machinery (BAM) complex of the OM of Gram-negative bacteria. Fluorescence spectroscopy was used to probe the interactions of BamD with lipid membranes and to investigate the interactions of BamD with possible partner proteins from the periplasm and from the OM. A range of single cysteine (Cys) and single tryptophan (Trp) mutants of BamD were prepared. A very important conclusion from the extensive FRET study is that the essential lipoprotein BamD interacts and binds to the periplasmic chaperone Skp. BamD contains tetratrico peptide repeat (TPR) motifs that are suggested to serve as docking sites for periplasmic chaperones such as Skp.

Productivity, demand and the home market effect

The causality between international trade and industrialization is still ambiguous. We consider a model of international trade with the Home Market Effect - with differences in income and productivity between sectors and between countries - in order to identify additional channels for determining the effects of international trade on industrialization. Introducing non-homothetic preferences and differences in productivity aids in the interpretation of any apparent paradoxes within international trade, such as the commercial relations between more populated countries like China and India and large economies such as the U.S. Population size, demand composition and productivity levels constitute the three main channels for determining the effects of international trade. Interactions among these channels define the results obtained in terms of industrialization, while welfare levels are always higher in relation to autarky.

Argument omissions in preschool Catalan and Spanish speaking children with SLI

El presente artículo describe tres estudios sobre la producción del verbo y la estructura argumental en niños con Trastorno Específico del Lenguaje (TEL) usando diferentes metodologías. El primero es un estudio observacional que usa una muestra de habla espontánea. El segundo usa una tarea experimental de denominación de oraciones como resultado de la observación de videos de acciones. El tercero comprende la tarea de denominación de oraciones con imágenes estáticas en eventos con diferente complejidad argumental. Aunque los datos concretos varían en función de la metodología usada, hay una clara evidencia de que los niños de habla catalana y española con TEL presentan especiales dificultades en la producción de verbos con una alta complejidad en relación a la estructura argumental y cometen errores en la especificación de los argumentos obligatorios. Se concluye que tanto limitaciones en el procesamiento como déficits en la representación semántica de los verbos pueden estar implicados en estas dificultades

The analysis of ranked observations of soil structure using indicator geostatistics

Structure is an important physical feature of the soil that is associated with water movement, the soil atmosphere, microorganism activity and nutrient uptake. A soil without any obvious organisation of its components is known as apedal and this state can have marked effects on several soil processes. Accurate maps of topsoil and subsoil structure are desirable for a wide range of models that aim to predict erosion, solute transport, or flow of water through the soil. Also such maps would be useful to precision farmers when deciding how to apply nutrients and pesticides in a site-specific way, and to target subsoiling and soil structure stabilization procedures. Typically, soil structure is inferred from bulk density or penetrometer resistance measurements and more recently from soil resistivity and conductivity surveys. To measure the former is both time-consuming and costly, whereas observations made by the latter methods can be made automatically and swiftly using a vehicle-mounted penetrometer or resistivity and conductivity sensors. The results of each of these methods, however, are affected by other soil properties, in particular moisture content at the time of sampling, texture, and the presence of stones. Traditional methods of observing soil structure identify the type of ped and its degree of development. Methods of ranking such observations from good to poor for different soil textures have been developed. Indicator variograms can be computed for each category or rank of structure and these can be summed to give the sum of indicator variograms (SIV). Observations of the topsoil and subsoil structure were made at four field sites where the soil had developed on different parent materials. The observations were ranked by four methods and indicator and the sum of indicator variograms were computed and modelled for each method of ranking. The individual indicators were then kriged with the parameters of the appropriate indicator variogram model to map the probability of encountering soil with the structure represented by that indicator. The model parameters of the SIVs for each ranking system were used with the data to krige the soil structure classes, and the results are compared with those for the individual indicators. The relations between maps of soil structure and selected wavebands from aerial photographs are examined as basis for planning surveys of soil structure. (C) 2007 Elsevier B.V. All rights reserved.

The ASSET intercomparison of ozone analyses: method and first results

This paper aims to summarise the current performance of ozone data assimilation (DA) systems, to show where they can be improved, and to quantify their errors. It examines 11 sets of ozone analyses from 7 different DA systems. Two are numerical weather prediction (NWP) systems based on general circulation models (GCMs); the other five use chemistry transport models (CTMs). The systems examined contain either linearised or detailed ozone chemistry, or no chemistry at all. In most analyses, MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) ozone data are assimilated; two assimilate SCIAMACHY (Scanning Imaging Absorption Spectrometer for Atmospheric Chartography) observations instead. Analyses are compared to independent ozone observations covering the troposphere, stratosphere and lower mesosphere during the period July to November 2003. Biases and standard deviations are largest, and show the largest divergence between systems, in the troposphere, in the upper-troposphere/lower-stratosphere, in the upper-stratosphere and mesosphere, and the Antarctic ozone hole region. However, in any particular area, apart from the troposphere, at least one system can be found that agrees well with independent data. In general, none of the differences can be linked to the assimilation technique (Kalman filter, three or four dimensional variational methods, direct inversion) or the system (CTM or NWP system). Where results diverge, a main explanation is the way ozone is modelled. It is important to correctly model transport at the tropical tropopause, to avoid positive biases and excessive structure in the ozone field. In the southern hemisphere ozone hole, only the analyses which correctly model heterogeneous ozone depletion are able to reproduce the near-complete ozone destruction over the pole. In the upper-stratosphere and mesosphere (above 5 hPa), some ozone photochemistry schemes caused large but easily remedied biases. The diurnal cycle of ozone in the mesosphere is not captured, except by the one system that includes a detailed treatment of mesospheric chemistry. These results indicate that when good observations are available for assimilation, the first priority for improving ozone DA systems is to improve the models. The analyses benefit strongly from the good quality of the MIPAS ozone observations. Using the analyses as a transfer standard, it is seen that MIPAS is similar to 5% higher than HALOE (Halogen Occultation Experiment) in the mid and upper stratosphere and mesosphere (above 30 hPa), and of order 10% higher than ozonesonde and HALOE in the lower stratosphere (100 hPa to 30 hPa). Analyses based on SCIAMACHY total column are almost as good as the MIPAS analyses; analyses based on SCIAMACHY limb profiles are worse in some areas, due to problems in the SCIAMACHY retrievals.

Quasi-biennial oscillation and tracer distributions in a coupled chemistry-climate model

[ 1] We have used a fully coupled chemistry-climate model (CCM), which generates its own wind and temperature quasi-biennial oscillation (QBO), to study the effect of coupling on the QBO and to examine the QBO signals in stratospheric trace gases, particularly ozone. Radiative coupling of the interactive chemistry to the underlying general circulation model tends to prolong the QBO period and to increase the QBO amplitude in the equatorial zonal wind in the lower and middle stratosphere. The model ozone QBO agrees well with Stratospheric Aerosol and Gas Experiment II and Total Ozone Mapping Spectrometer satellite observations in terms of vertical and latitudinal structure. The model captures the ozone QBO phase change near 28 km over the equator and the column phase change near +/- 15 degrees latitude. Diagnosis of the model chemical terms shows that variations in NOx are the main chemical driver of the O-3 QBO around 35 km, i.e., above the O-3 phase change.

Temperature-responsive properties and drug solubilization capacity of amphiphilic copolymers based on N-vinylpyrrolidone and vinyl propyl ether

A series of amphiphilic copolymers were synthesized by free-radical copolymerization of N-vinylpyrrolidone (NVP) with vinyl propyl ether (VPE), and the structure of the copolymers was characterized by elemental analysis and gel permeation chromatography. The reactivity of VPE in copolymerization was found to be significantly lower than the reactivity of NVP, which resulted in a decrease of copolymers’ yields and molecular weights with higher content of VPE in the feed mixture. An investigation of the behavior of the copolymers in aqueous solutions at different temperatures by dynamic light scattering revealed the presence of lower critical solution temperature, which depending on the content of VPE ranged within 23−38 °C. Aqueous solutions of these copolymers were studied by fluorescent spectroscopy with pyrene as a polarity probe to reveal the formation of hydrophobic domains. The copolymers were found to be useful for enhancing the solubility of riboflavin in water.

The assessment of benchmarks executed on bare-metal and using para-virtualization

A full assessment of para-­virtualization is important, because without knowledge about the various overheads, users can not understand whether using virtualization is a good idea or not. In this paper we are very interested in assessing the overheads of running various benchmarks on bare-­‐metal, as well as on para-­‐virtualization. The idea is to see what the overheads of para-­‐ virtualization are, as well as looking at the overheads of turning on monitoring and logging. The knowledge from assessing various benchmarks on these different systems will help a range of users understand the use of virtualization systems. In this paper we assess the overheads of using Xen, VMware, KVM and Citrix, see Table 1. These different virtualization systems are used extensively by cloud-­‐users. We are using various Netlib1 benchmarks, which have been developed by the University of Tennessee at Knoxville (UTK), and Oak Ridge National Laboratory (ORNL). In order to assess these virtualization systems, we run the benchmarks on bare-­‐metal, then on the para-­‐virtualization, and finally we turn on monitoring and logging. The later is important as users are interested in Service Level Agreements (SLAs) used by the Cloud providers, and the use of logging is a means of assessing the services bought and used from commercial providers. In this paper we assess the virtualization systems on three different systems. We use the Thamesblue supercomputer, the Hactar cluster and IBM JS20 blade server (see Table 2), which are all servers available at the University of Reading. A functional virtualization system is multi-­‐layered and is driven by the privileged components. Virtualization systems can host multiple guest operating systems, which run on its own domain, and the system schedules virtual CPUs and memory within each Virtual Machines (VM) to make the best use of the available resources. The guest-­‐operating system schedules each application accordingly. You can deploy virtualization as full virtualization or para-­‐virtualization. Full virtualization provides a total abstraction of the underlying physical system and creates a new virtual system, where the guest operating systems can run. No modifications are needed in the guest OS or application, e.g. the guest OS or application is not aware of the virtualized environment and runs normally. Para-­‐virualization requires user modification of the guest operating systems, which runs on the virtual machines, e.g. these guest operating systems are aware that they are running on a virtual machine, and provide near-­‐native performance. You can deploy both para-­‐virtualization and full virtualization across various virtualized systems. Para-­‐virtualization is an OS-­‐assisted virtualization; where some modifications are made in the guest operating system to enable better performance. In this kind of virtualization, the guest operating system is aware of the fact that it is running on the virtualized hardware and not on the bare hardware. In para-­‐virtualization, the device drivers in the guest operating system coordinate the device drivers of host operating system and reduce the performance overheads. The use of para-­‐virtualization [0] is intended to avoid the bottleneck associated with slow hardware interrupts that exist when full virtualization is employed. It has revealed [0] that para-­‐ virtualization does not impose significant performance overhead in high performance computing, and this in turn this has implications for the use of cloud computing for hosting HPC applications. The “apparent” improvement in virtualization has led us to formulate the hypothesis that certain classes of HPC applications should be able to execute in a cloud environment, with minimal performance degradation. In order to support this hypothesis, first it is necessary to define exactly what is meant by a “class” of application, and secondly it will be necessary to observe application performance, both within a virtual machine and when executing on bare hardware. A further potential complication is associated with the need for Cloud service providers to support Service Level Agreements (SLA), so that system utilisation can be audited.

Pollination and other ecosystem services produced by mobile organisms: a conceptual framework for the effects of land-use change

Many ecosystem services are delivered by organisms that depend on habitats that are segregated spatially or temporally from the location where services are provided. Management of mobile organisms contributing to ecosystem services requires consideration not only of the local scale where services are delivered, but also the distribution of resources at the landscape scale, and the foraging ranges and dispersal movements of the mobile agents. We develop a conceptual model for exploring how one such mobile-agent-based ecosystem service (MABES), pollination, is affected by land-use change, and then generalize the model to other MABES. The model includes interactions and feedbacks among policies affecting land use, market forces and the biology of the organisms involved. Animal-mediated pollination contributes to the production of goods of value to humans such as crops; it also bolsters reproduction of wild plants on which other services or service-providing organisms depend. About one-third of crop production depends on animal pollinators, while 60-90% of plant species require an animal pollinator. The sensitivity of mobile organisms to ecological factors that operate across spatial scales makes the services provided by a given community of mobile agents highly contextual. Services vary, depending on the spatial and temporal distribution of resources surrounding the site, and on biotic interactions occurring locally, such as competition among pollinators for resources, and among plants for pollinators. The value of the resulting goods or services may feed back via market-based forces to influence land-use policies, which in turn influence land management practices that alter local habitat conditions and landscape structure. Developing conceptual models for MABES aids in identifying knowledge gaps, determining research priorities, and targeting interventions that can be applied in an adaptive management context.

Effects of seed mixture and management on beetle assemblages of arable field margins

Beetle assemblages and their response to plant community composition and architectural structure were monitored from 2002 to 2006 within arable field margins. Field margins were sown with either tussock grass and forbs, fine grass and forbs or grass only seed mixtures. After an establishment year, field margins were managed using standard sward cuts, scarification, or graminicide application. For predatory beetles, overall density was greatest where tussock grasses were included within the seed mixtures, while the densities of phytophagous beetles were greatest where forbs were present. Unexpectedly, species rarefaction curves suggested that phytophagous beetle species richness was greatest where field margins were established using a grass only seed mixture. The structure of the beetle assemblages, i.e., the relative abundances of individual species, was largely dependent on seed mixture, although margin management also played an important role. The results suggest that field margins established using seed mixtures containing tussock grasses and forbs would be expected to provide the greatest resources for beetles, at least at local scales. However, the use of a single standardised seed mixture for margin establishment would result in a homogenisation of beetle assemblages at a regional scale. (C) 2008 Elsevier B.V. All rights reserved.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Anthraquinone catalysis in the glucose-driven reduction of indigo to leuco-indigo

Anthraquinone immobilised onto the surface of indigo microcrystals enhances the reductive dissolution of indigo to leuco-indigo. Indigo reduction is driven by glucose in aqueous NaOH and a vibrating gold disc electrode is employed to monitor the increasing leuco-indigo concentration with time. Anthraquinone introduces a strong catalytic effect which is explained by invoking a molecular "wedge effect'' during co-intercalation of Na+ and anthraquinone into the layered indigo crystal structure. The glucose-driven indigo reduction, which is in effective in 0.1 M NaOH at 65 degrees C, becomes facile and goes to completion in the presence of anthraquinone catalyst. Electron microscopy of indigo crystals before and after reductive dissolution confirms a delamination mechanism initiated at the edges of the plate-like indigo crystals. Catalysis occurs when the anthraquinone-indigo mixture reaches a molar ratio of 1:400 (at 65 degrees C; corresponding to 3 mu M anthraquinone) with excess of anthraquinone having virtually no effect. A strong temperature effect ( with a composite E-A approximate to 120 kJ mol(-1)) is observed for the reductive dissolution in the presence of anthraquinone. The molar ratio and temperature effects are both consistent with the heterogeneous nature of the anthraquinone catalysis in the aqueous reaction mixture.