Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae

Background Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the characteristic aroma of the fruit. These compounds are formed from unsaturated fatty acids through oxidation, pyrolysis and reduction steps. This biosynthetic pathway involves at least four enzymes, including LOX, the enzyme responsible for lipid oxidation. Although some studies have been conducted on the LOX gene family in several species including Arabidopsis, soybean, cucumber and apple, there is no information from pear; and the evolutionary history of this gene family in the Rosaceae is still not resolved. Results In this study we identified 107 LOX homologous genes from five Rosaceous species (Pyrus bretschneideri, Malus × domestica, Fragaria vesca, Prunus mume and Prunus persica); 23 of these sequences were from pear. By using structure analysis, phylogenic analysis and collinearity analysis, we identified variation in gene structure and revealed the phylogenetic evolutionary relationship of this gene family. Expression of certain pear LOX genes during fruit development was verified by analysis of transcriptome data. Conclusions 23 LOX genes were identified in pear and these genes were found to have undergone a duplication 30–45 MYA; most of these 23 genes are functional. Specific gene duplication was found on chromosome4 in the pear genome. Useful information was provided for future research on the evolutionary history and transgenic research on LOX genes.

First structural analysis of a naphthalene-based poly(ether ketone): Crystal and molecular simulation from X-ray powder data and diffraction modeling

Polycondensation of 2,6-dihydroxynaphthalene with 4,4'-bis(4"-fluorobenzoyl)biphenyl affords a novel, semicrystalline poly(ether ketone) with a melting point of 406 degreesC and glass transition temperature (onset) of 168 degreesC. Molecular modeling and diffraction-simulation studies of this polymer, coupled with data from the single-crystal structure of an oligomer model, have enabled the crystal and molecular structure of the polymer to be determined from X-ray powder data. This structure-the first for any naphthalene-containing poly(ether ketone)-is fully ordered, in monoclinic space group P2(1)/b, with two chains per unit cell. Rietveld refinement against the experimental powder data gave a final agreement factor (R-wp) of 6.7%.

A semi-quantitative approach to deriving a model structure for the uptake of organic chemicals by vegetation

An expert elicitation exercise was undertaken to determine those components and processes that are most important for modeling plant uptake of organic chemicals. The state of our knowledge of these processes was also assessed. This semi-quantitative analysis allowed the construction of an idealized model with seven compartments; soil bulk, soil water, roots, stem, leaves, fruit, and air. Three main areas were identified further research: 1) the uptake of organic chemicals by fruit; 2) the internal transfer of organic chemicals between plant structures (e.g., stem and leaves); and 3) the transfer via the soil-air-plant pathway. Until new data becomes available to quantify these processes, it is proposed that an equilibrium partitioning approach is used between plant components other than fruit or that models consist of both an edible and inedible compartment.

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.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

The poliovirus cis-acting replication element (CRE) templates the uridylylation of VPg, the protein primer for genome replication. The CRE is a highly conserved structural RNA element in the enteroviruses and located within the polyprotein-coding region of the genome. We have determined the native structure of the CRE, defined the regions of the structure critical for activity, and investigated the influence of genomic location on function. Our results demonstrate that a 14-nucleotide unpaired terminal loop, presented on a suitably stable stem, is all that is required for function. These conclusions complement the recent analysis of the 14-nucleotide terminal loop in the CRE of human rhinovirus type 14. The CRE can be translocated to the 5' noncoding region of the genome, at least 3.7-kb distant from the native location, without adversely influencing activity, and CRE duplications do not adversely influence replication. We do not have evidence for a specific interaction between the CRE and the RNA-binding 3CD(pro) complex, an essential component of the uridylylation reaction, and the mechanism by which the CRE is coordinated and orientated during the reaction remains unclear. These studies provide a detailed overview of the structural determinants required for CRE function, and will facilitate a better understanding of the requirements for picornavirus replication.

Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains Of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo-3 triangular clusters in accounting for the available experimental data.

Applying semiotic analysis to the design and modeling of distributed multimedia systems

Semiotics is the study of signs. Application of semiotics in information systems design is based on the notion that information systems are organizations within which agents deploy signs in the form of actions according to a set of norms. An analysis of the relationships among the agents, their actions and the norms would give a better specification of the system. Distributed multimedia systems (DMMS) could be viewed as a system consisted of many dynamic, self-controlled normative agents engaging in complex interaction and processing of multimedia information. This paper reports the work of applying the semiotic approach to the design and modeling of DMMS, with emphasis on using semantic analysis under the semiotic framework. A semantic model of DMMS describing various components and their ontological dependencies is presented, which then serves as a design model and implemented in a semantic database. Benefits of using the semantic database are discussed with reference to various design scenarios.

Tracking and mean structure of easterly waves over the Intra-Americas Sea

Easterly waves (EWs) are prominent features of the intertropical convergence zone (ITCZ), found in both the Atlantic and Pacific during the Northern Hemisphere summer and fall, where they commonly serve as precursors to hurricanes over both basins.Alarge proportion of Atlantic EWs are known to form over Africa, but the origin of EWs over the Caribbean and east Pacific in particular has not been established in detail. In this study reanalyses are used to examine the coherence of the large-scale wave signatures and to obtain track statistics and energy conversion terms for EWs across this region. Regression analysis demonstrates that some EW kinematic structures readily propagate between the Atlantic and east Pacific, with the highest correlations observed across Costa Rica and Panama. Track statistics are consistent with this analysis and suggest that some individual waves are maintained as they pass from the Atlantic into the east Pacific, whereas others are generated locally in the Caribbean and east Pacific. Vortex anomalies associated with the waves are observed on the leeward side of the Sierra Madre, propagating northwestward along the coast, consistent with previous modeling studies of the interactions between zonal flow and EWs with model topography similar to the Sierra Madre. An energetics analysis additionally indicates that the Caribbean low-level jet and its extension into the east Pacific—known as the Papagayo jet—are a source of energy for EWs in the region. Two case studies support these statistics, as well as demonstrate the modulation of EW track and storm development location by the MJO.

The relation between content and structure in language production: an analysis of speech errors in semantic dementia

In order to explore the impact of a degraded semantic system on the structure of language production, we analysed transcripts from autobiographical memory interviews to identify naturally-occurring speech errors by eight patients with semantic dementia (SD) and eight age-matched normal speakers. Relative to controls, patients were significantly more likely to (a) substitute and omit open class words, (b) substitute (but not omit) closed class words, (c) substitute incorrect complex morphological forms and (d) produce semantically and/or syntactically anomalous sentences. Phonological errors were scarce in both groups. The study confirms previous evidence of SD patients’ problems with open class content words which are replaced by higher frequency, less specific terms. It presents the first evidence that SD patients have problems with closed class items and make syntactic as well as semantic speech errors, although these grammatical abnormalities are mostly subtle rather than gross. The results can be explained by the semantic deficit which disrupts the representation of a pre-verbal message, lexical retrieval and the early stages of grammatical encoding.

Algorithmic statistical analysis of electrophysiological data for the investigation of structure-activity relationship in single neurons

We are developing computational tools supporting the detailed analysis of the dependence of neural electrophysiological response on dendritic morphology. We approach this problem by combining simulations of faithful models of neurons (experimental real life morphological data with known models of channel kinetics) with algorithmic extraction of morphological and physiological parameters and statistical analysis. In this paper, we present the novel method for an automatic recognition of spike trains in voltage traces, which eliminates the need for human intervention. This enables classification of waveforms with consistent criteria across all the analyzed traces and so it amounts to reduction of the noise in the data. This method allows for an automatic extraction of relevant physiological parameters necessary for further statistical analysis. In order to illustrate the usefulness of this procedure to analyze voltage traces, we characterized the influence of the somatic current injection level on several electrophysiological parameters in a set of modeled neurons. This application suggests that such an algorithmic processing of physiological data extracts parameters in a suitable form for further investigation of structure-activity relationship in single neurons.

Modeling camera orientation and 3D structure from a sequence of images taken by a perambulating commercial video camera

In this paper we report the degree of reliability of image sequences taken by off-the-shelf TV cameras for modeling camera rotation and reconstructing 3D structure using computer vision techniques. This is done in spite of the fact that computer vision systems usually use imaging devices that are specifically designed for the human vision. Our scenario consists of a static scene and a mobile camera moving through the scene. The scene is any long axial building dominated by features along the three principal orientations and with at least one wall containing prominent repetitive planar features such as doors, windows bricks etc. The camera is an ordinary commercial camcorder moving along the axial axis of the scene and is allowed to rotate freely within the range +/- 10 degrees in all directions. This makes it possible that the camera be held by a walking unprofessional cameraman with normal gait, or to be mounted on a mobile robot. The system has been tested successfully on sequence of images of a variety of structured, but fairly cluttered scenes taken by different walking cameramen. The potential application areas of the system include medicine, robotics and photogrammetry.

The distribution of solar wind speeds during solar minimum: calibration for numerical solar wind modeling constraints on the source of the slow solar wind

It took the solar polar passage of Ulysses in the early 1990s to establish the global structure of the solar wind speed during solar minimum. However, it remains unclear if the solar wind is composed of two distinct populations of solar wind from different sources (e.g., closed loops which open up to produce the slow solar wind) or if the fast and slow solar wind rely on the superradial expansion of the magnetic field to account for the observed solar wind speed variation. We investigate the solar wind in the inner corona using the Wang-Sheeley-Arge (WSA) coronal model incorporating a new empirical magnetic topology–velocity relationship calibrated for use at 0.1 AU. In this study the empirical solar wind speed relationship was determined by using Helios perihelion observations, along with results from Riley et al. (2003) and Schwadron et al. (2005) as constraints. The new relationship was tested by using it to drive the ENLIL 3-D MHD solar wind model and obtain solar wind parameters at Earth (1.0 AU) and Ulysses (1.4 AU). The improvements in speed, its variability, and the occurrence of high-speed enhancements provide confidence that the new velocity relationship better determines the solar wind speed in the outer corona (0.1 AU). An analysis of this improved velocity field within the WSA model suggests the existence of two distinct mechanisms of the solar wind generation, one for fast and one for slow solar wind, implying that a combination of present theories may be necessary to explain solar wind observations.

Analysis and modeling of ants’ behavior from single to multi-body

In order to shed light on the collective behavior of social insects, we analyzed the behavior of ants from single to multi-body. In an experimental set-up, ants are placed in hemisphere without a nest and food. Trajectory of ants is recorded. From this bottom-up approach, we found that collective behavior of ants as follows: 1. Activity of single ant increases and decreases periodically. 2. Spontaneous meeting process is observed between two ants and meeting spot of two ants is localized in hemisphere. 3. Result on division of labor is obtained between two ants.

Analysis and modeling of active occupancy of the residential sector in Spain: an indicator of residential electricity consumption

The growing energy consumption in the residential sector represents about 30% of global demand. This calls for Demand Side Management solutions propelling change in behaviors of end consumers, with the aim to reduce overall consumption as well as shift it to periods in which demand is lower and where the cost of generating energy is lower. Demand Side Management solutions require detailed knowledge about the patterns of energy consumption. The profile of electricity demand in the residential sector is highly correlated with the time of active occupancy of the dwellings; therefore in this study the occupancy patterns in Spanish properties was determined using the 2009–2010 Time Use Survey (TUS), conducted by the National Statistical Institute of Spain. The survey identifies three peaks in active occupancy, which coincide with morning, noon and evening. This information has been used to input into a stochastic model which generates active occupancy profiles of dwellings, with the aim to simulate domestic electricity consumption. TUS data were also used to identify which appliance-related activities could be considered for Demand Side Management solutions during the three peaks of occupancy.