Isolation of culturable yeasts from market wines and evaluation of the 5 center dot 8S-ITS rDNA sequence analysis for identification purposes

Aims: To test the possibility that wines available in the marketplace may contain culturable yeasts and to evaluate the 5.8S-ITS rDNA sequence analysis as adequate means for the identification of isolates. Methods and Results: As a case study, typical Greek wines were surveyed. Sequence analysis of the 5.8S-ITS rDNA was tested for its robustness in species or strain identification. Sixteen isolates could be assigned into the species Brettanomyces bruxellensis, Saccharomyces cerevisiae and Rhodotorula pinicola, whereas four isolates could not be safely identified. B. bruxellensis was the dominant species present in house wines, while non-Saccharomyces sp. were viable in aged wines of high alcohol content. Conclusions: Yeast population depends on postfermentation procedures or storage conditions. Although 5.8S-ITS rDNA sequence analysis is generally a rapid method to identify wine yeast isolates at the species level, or even below that, it may not be sufficient for some genera. Significance and Impact of the Study: This is the first report to show that commercial wines may possess diverse and potentially harmful yeast populations. The knowledge of yeasts able to reside in this niche environment is essential towards integrated quality assurance programmes. For selected species, the 5.8S-ITS rDNA sequence analysis is a rapid and accurate means.

Fecal water as a non-invasive biomarker in nutritional intervention: comparison of preparation methods and refinement of different endpoints

The assessment of cellular effects by the aqueous phase of human feces (fecal water, FW) is a useful biomarker approach to study cancer risks and protective activities of food. In order to refine and develop the biomarker, different protocols of preparing FW were compared. Fecal waters were prepared by 3 methods: (A) direct centrifugation; (B) extraction of feces in PBS before centrifugation; and (C) centrifugation of lyophilized and reconstituted feces. Genotoxicity was determined in colon cells using the Comet assay. Selected samples were investigated for additional parameters related to carcinogenesis. Two of 7 FWs obtained by methods A and B were similarly genotoxic. Method B, however, yielded higher volumes of FW, allowing sterile filtration for long-term culture experiments. Four of 7 samples were non-genotoxic when prepared according to all 3 methods. FW from lyophilized feces and from fresh samples were equally genotoxic. FWs modulated cytotoxicity, paracellular permeability, and invasion, independent of their genotoxicity. All 3 methods of FW preparation can be used to assess genotoxicity. The higher volumes of FWobtained by preparation method B greatly enhance the perspectives of measuring different types of biological parameters and using these to disclose activities related to cancer development.

Ontological modelling of content management and provision

Information provision to address the changing requirements can be best supported by content management. The Current information technology enables information to be stored and provided from various distributed sources. To identify and retrieve relevant information requires effective mechanisms for information discovery and assembly. This paper presents a method, which enables the design of such mechanisms, with a set of techniques for articulating and profiling users' requirements, formulating information provision specifications, realising management of information content in repositories, and facilitating response to the user's requirements dynamically during the process of knowledge construction. These functions are represented in an ontology which integrates the capability of the mechanisms. The ontological modelling in this paper has adopted semiotics principles with embedded norms to ensure coherent course of actions represented in these mechanisms. (C) 2008 Elsevier B.V. All rights reserved.

Semantic-associative visual content labelling and retrieval: A multimodal approach

A novel framework referred to as collaterally confirmed labelling (CCL) is proposed, aiming at localising the visual semantics to regions of interest in images with textual keywords. Both the primary image and collateral textual modalities are exploited in a mutually co-referencing and complementary fashion. The collateral content and context-based knowledge is used to bias the mapping from the low-level region-based visual primitives to the high-level visual concepts defined in a visual vocabulary. We introduce the notion of collateral context, which is represented as a co-occurrence matrix of the visual keywords. A collaborative mapping scheme is devised using statistical methods like Gaussian distribution or Euclidean distance together with collateral content and context-driven inference mechanism. We introduce a novel high-level visual content descriptor that is devised for performing semantic-based image classification and retrieval. The proposed image feature vector model is fundamentally underpinned by the CCL framework. Two different high-level image feature vector models are developed based on the CCL labelling of results for the purposes of image data clustering and retrieval, respectively. A subset of the Corel image collection has been used for evaluating our proposed method. The experimental results to-date already indicate that the proposed semantic-based visual content descriptors outperform both traditional visual and textual image feature models. (C) 2007 Elsevier B.V. All rights reserved.

Collaterally cued labelling framework underpinning semantic-level visual content descriptor

In this paper, we introduce a novel high-level visual content descriptor devised for performing semantic-based image classification and retrieval. The work can be treated as an attempt for bridging the so called "semantic gap". The proposed image feature vector model is fundamentally underpinned by an automatic image labelling framework, called Collaterally Cued Labelling (CCL), which incorporates the collateral knowledge extracted from the collateral texts accompanying the images with the state-of-the-art low-level visual feature extraction techniques for automatically assigning textual keywords to image regions. A subset of the Corel image collection was used for evaluating the proposed method. The experimental results indicate that our semantic-level visual content descriptors outperform both conventional visual and textual image feature models.

Flux difference splitting for inviscid, real gases with non-equilibrium chemistry

A flux-difference splitting method is presented for the inviscid terms of the compressible flow equations for chemical non-equilibrium gases

Numerical modelling of two-way propagation of non-linear dispersive waves

We describe and implement a fully discrete spectral method for the numerical solution of a class of non-linear, dispersive systems of Boussinesq type, modelling two-way propagation of long water waves of small amplitude in a channel. For three particular systems, we investigate properties of the numerically computed solutions; in particular we study the generation and interaction of approximate solitary waves.

Sex allocation and local mate competition in Old World non-pollinating fig wasps

The populations of many species are structured such that mating is not random and occurs between members of local patches. When patches are founded by a single female and all matings occur between siblings, brothers may compete with each other for matings with their sisters. This local mate competition (LMC) selects for a female-biased sex ratio, especially in species where females have control over offspring sex, as in the parasitic Hymenoptera. Two factors are predicted to decrease the degree of female bias: (1) an increase in the number of foundress females in the patch and (2) an increase in the fraction of individuals mating after dispersal from the natal patch. Pollinating fig wasps are well known as classic examples of species where all matings occur in the local patch. We studied non-pollinating fig wasps, which are more diverse than the pollinating fig wasps and also provide natural experimental groups of species with different male morphologies that are linked to different mating structures. In this group of wasps, species with wingless males mate in the local patch (i.e. the fig fruit) while winged male species mate after dispersal. Species with both kinds of male have a mixture of local and non-local mating. Data from 44 species show that sex ratios (defined as the proportion of males) are in accordance with theoretical predictions: wingless male species < wing-dimorphic male species < winged male species. These results are also supported by a formal comparative analysis that controls for phylogeny. The foundress number is difficult to estimate directly for non-pollinating fig wasps but a robust indirect method leads to the prediction that foundress number, and hence sex ratio, should increase with the proportion of patches occupied in a crop. This result is supported strongly across 19 species with wingless males, but not across 8 species with winged males. The mean sex ratios for species with winged males are not significantly different from 0.5, and the absence of the correlation observed across species with wingless males may reflect weak selection to adjust the sex ratio in species whose population mating structure tends not to be subdivided. The same relationship is also predicted to occur within species if individual females adjust their sex ratios facultatively. This final prediction was not supported by data from a wingless male species, a male wing-dimorphic species or a winged male species.

Synthesis method for visible and infrared broadband spaceflight antireflection coatings

Evolutionary synthesis methods, as originally described by Dobrowolski, have been shown in previous literature to be an effective method of obtaining anti-reflection coating designs. To make this method even more effective, the combination of a good starting design, the best suited thin-film materials, a realistic optimization target function and a non-gradient optimization method are used in an algorithm written for a PC. Several broadband anti-reflection designs obtained by this new design method are given as examples of its usefulness.

Low-order dynamical behavior in the martian atmosphere: Diagnosis of general circulation model results

The hypothesis of a low dimensional martian climate attractor is investigated by the application of the proper orthogonal decomposition (POD) to a simulation of martian atmospheric circulation using the UK Mars general circulation model (UK-MGCM). In this article we focus on a time series of the interval between autumn and winter in the northern hemisphere, when baroclinic activity is intense. The POD is a statistical technique that allows the attribution of total energy (TE) to particular structures embedded in the UK-MGCM time-evolving circulation. These structures are called empirical orthogonal functions (EOFs). Ordering the EOFs according to their associated energy content, we were able to determine the necessary number to account for a chosen amount of atmospheric TE. We show that for Mars a large fraction of TE is explained by just a few EOFs (with 90% TE in 23 EOFs), which apparently support the initial hypothesis. We also show that the resulting EOFs represent classical types of atmospheric motion, such as thermal tides and transient waves. Thus, POD is shown to be an efficient method for the identification of different classes of atmospheric modes. It also provides insight into the non-linear interaction of these modes.

Composite control of non-linear singularly perturbed systems: meeting a design objective

Using the integral manifold approach, a composite control—the sum of a fast control and a slow control—is derived for a particular class of non-linear singularly perturbed systems. The fast control is designed completely at the outset, thus ensuring the stability of the fast transients of the system and, furthermore, the existence of the integral manifold. A new method is then presented which simplifies the derivation of a slow control such that the singularly perturbed system meets a preselected design objective to within some specified order of accuracy. Though this approach is, by its very nature, ad hoc, the underlying procedure is easily extended to more general classes of singularly perturbed systems by way of three examples.

Technologies for biological containment of GM and Non-GM crops

International Perspective The development of GM technology continues to expand into increasing numbers of crops and conferred traits. Inevitably, the focus remains on the major field crops of soybean, maize, cotton, oilseed rape and potato with introduced genes conferring herbicide tolerance and/or pest resistance. Although there are comparatively few GM crops that have been commercialised to date, GM versions of 172 plant species have been grown in field trials in 31 countries. European Crops with Containment Issues Of the 20 main crops in the EU there are four for which GM varieties are commercially available (cotton, maize for animal feed and forage, and oilseed rape). Fourteen have GM varieties in field trials (bread wheat, barley, durum wheat, sunflower, oats, potatoes, sugar beet, grapes, alfalfa, olives, field peas, clover, apples, rice) and two have GM varieties still in development (rye, triticale). Many of these crops have hybridisation potential with wild and weedy relatives in the European flora (bread wheat, barley, oilseed rape, durum wheat, oats, sugar beet and grapes), with escapes (sunflower); and all have potential to cross-pollinate fields non-GM crops. Several fodder crops, forestry trees, grasses and ornamentals have varieties in field trials and these too may hybridise with wild relatives in the European flora (alfalfa, clover, lupin, silver birch, sweet chestnut, Norway spruce, Scots pine, poplar, elm, Agrostis canina, A. stolonifera, Festuca arundinacea, Lolium perenne, L. multiflorum, statice and rose). All these crops will require containment strategies to be in place if it is deemed necessary to prevent transgene movement to wild relatives and non-GM crops. Current Containment Strategies A wide variety of GM containment strategies are currently under development, with a particular focus on crops expressing pharmaceutical products. Physical containment in greenhouses and growth rooms is suitable for some crops (tomatoes, lettuce) and for research purposes. Aquatic bioreactors of some non-crop species (algae, moss, and duckweed) expressing pharmaceutical products have been adopted by some biotechnology companies. There are obvious limitations of the scale of physical containment strategies, addressed in part by the development of large underground facilities in the US and Canada. The additional resources required to grow plants underground incurs high costs that in the long term may negate any advantage of GM for commercial productioNatural genetic containment has been adopted by some companies through the selection of either non-food/feed crops (algae, moss, duckweed) as bio-pharming platforms or organisms with no wild relatives present in the local flora (safflower in the Americas). The expression of pharmaceutical products in leafy crops (tobacco, alfalfa, lettuce, spinach) enables growth and harvesting prior to and in the absence of flowering. Transgenically controlled containment strategies range in their approach and degree of development. Plastid transformation is relatively well developed but is not suited to all traits or crops and does not offer complete containment. Male sterility is well developed across a range of plants but has limitations in its application for fruit/seed bearing crops. It has been adopted in some commercial lines of oilseed rape despite not preventing escape via seed. Conditional lethality can be used to prevent flowering or seed development following the application of a chemical inducer, but requires 100% induction of the trait and sufficient application of the inducer to all plants. Equally, inducible expression of the GM trait requires equally stringent application conditions. Such a method will contain the trait but will allow the escape of a non-functioning transgene. Seed lethality (‘terminator’ technology) is the only strategy at present that prevents transgene movement via seed, but due to public opinion against the concept it has never been trialled in the field and is no longer under commercial development. Methods to control flowering and fruit development such as apomixis and cleistogamy will prevent crop-to-wild and wild-to-crop pollination, but in nature both of these strategies are complex and leaky. None of the genes controlling these traits have as yet been identified or characterised and therefore have not been transgenically introduced into crop species. Neither of these strategies will prevent transgene escape via seed and any feral apomicts that form are arguably more likely to become invasives. Transgene mitigation reduces the fitness of initial hybrids and so prevents stable introgression of transgenes into wild populations. However, it does not prevent initial formation of hybrids or spread to non-GM crops. Such strategies could be detrimental to wild populations and have not yet been demonstrated in the field. Similarly, auxotrophy prevents persistence of escapes and hybrids containing the transgene in an uncontrolled environment, but does not prevent transgene movement from the crop. Recoverable block of function, intein trans-splicing and transgene excision all use recombinases to modify the transgene in planta either to induce expression or to prevent it. All require optimal conditions and 100% accuracy to function and none have been tested under field conditions as yet. All will contain the GM trait but all will allow some non-native DNA to escape to wild populations or to non-GM crops. There are particular issues with GM trees and grasses as both are largely undomesticated, wind pollinated and perennial, thus providing many opportunities for hybridisation. Some species of both trees and grass are also capable of vegetative propagation without sexual reproduction. There are additional concerns regarding the weedy nature of many grass species and the long-term stability of GM traits across the life span of trees. Transgene stability and conferred sterility are difficult to trial in trees as most field trials are only conducted during the juvenile phase of tree growth. Bio-pharming of pharmaceutical and industrial compounds in plants Bio-pharming of pharmaceutical and industrial compounds in plants offers an attractive alternative to mammalian-based pharmaceutical and vaccine production. Several plantbased products are already on the market (Prodigene’s avidin, β-glucuronidase, trypsin generated in GM maize; Ventria’s lactoferrin generated in GM rice). Numerous products are in clinical trials (collagen, antibodies against tooth decay and non-Hodgkin’s lymphoma from tobacco; human gastric lipase, therapeutic enzymes, dietary supplements from maize; Hepatitis B and Norwalk virus vaccines from potato; rabies vaccines from spinach; dietary supplements from Arabidopsis). The initial production platforms for plant-based pharmaceuticals were selected from conventional crops, largely because an established knowledge base already existed. Tobacco and other leafy crops such as alfalfa, lettuce and spinach are widely used as leaves can be harvested and no flowering is required. Many of these crops can be grown in contained greenhouses. Potato is also widely used and can also be grown in contained conditions. The introduction of morphological markers may aid in the recognition and traceability of crops expressing pharmaceutical products. Plant cells or plant parts may be transformed and maintained in culture to produce recombinant products in a contained environment. Plant cells in suspension or in vitro, roots, root cells and guttation fluid from leaves may be engineered to secrete proteins that may be harvested in a continuous, non-destructive manner. Most strategies in this category remain developmental and have not been commercially adopted at present. Transient expression produces GM compounds from non-GM plants via the utilisation of bacterial or viral vectors. These vectors introduce the trait into specific tissues of whole plants or plant parts, but do not insert them into the heritable genome. There are some limitations of scale and the field release of such crops will require the regulation of the vector. However, several companies have several transiently expressed products in clinical and pre-clinical trials from crops raised in physical containment.

Periodic time series modeling of environmental proxy records with guaranteed positive growth rate estimation

Identifying a periodic time-series model from environmental records, without imposing the positivity of the growth rate, does not necessarily respect the time order of the data observations. Consequently, subsequent observations, sampled in the environmental archive, can be inversed on the time axis, resulting in a non-physical signal model. In this paper an optimization technique with linear constraints on the signal model parameters is proposed that prevents time inversions. The activation conditions for this constrained optimization are based upon the physical constraint of the growth rate, namely, that it cannot take values smaller than zero. The actual constraints are defined for polynomials and first-order splines as basis functions for the nonlinear contribution in the distance-time relationship. The method is compared with an existing method that eliminates the time inversions, and its noise sensitivity is tested by means of Monte Carlo simulations. Finally, the usefulness of the method is demonstrated on the measurements of the vessel density, in a mangrove tree, Rhizophora mucronata, and the measurement of Mg/Ca ratios, in a bivalve, Mytilus trossulus.