Limnological characteristics and zooplankton community structure of Mediterranean coastal lagoons undergoing restoration

Entre 1999 i 2003 es va desenvolupar un projecte Life de restauració a la maresma de La Pletera, afectada per un pla urbanització, i a la llacuna del Ter Vell, amb un elevat grau d'eutròfia (aiguamolls del Baix Ter, NE Península Ibèrica). L'objectiu d'aquesta tesi és establir el funcionament d'ambdós ecosistemes, analitzar-ne la problemàtica ambiental i avaluar els efectes de la restauració. A la maresma de la Pletera, es va analitzar el paper de la hidrologia en la composició i dinàmica dels nutrients i del zooplàncton en cinc llacunes, tres de les quals havien estat creades dins el projecte de restauració com a nous refugis per una espècie de peix amenaçada (Aphanius iberus). La hidrologia es va caracteritzar per un llarg període de confinament sense entrades d'aigua, interromput de manera irregular per inundacions puntuals. La dinàmica del nitrogen inorgànic es va relacionar amb les entrades d'aigua, mentre que la del fòsfor, del nitrogen total i de la matèria orgànica es va relacionar amb els processos d'acumulació i reciclatge intern durant el confinament. El zooplàncton es va analitzar mitjançant la combinació d'aproximacions taxonòmiques i de mides. L'estructura de mides de la comunitat es va veure més afectada per les interaccions tròfiques (depredació i competència) mentre que l'estructura taxonòmica va ser més sensible a factors abiòtics (nutrients). El ràpid creixement de la població A. iberus en les noves llacunes va suggerir que aquestes havien proporcionat l'hàbitat adequat per a l'espècie, almenys a curt termini. Les actuacions de restauració a la llacuna del Ter Vell es van centrar en la millora de la qualitat de l'aigua mitjançant (1) la construcció d'uns aiguamolls per depurar l'aigua d'entrada i (2) el dragat del sediment en diversos punts. Simultàniament a la restauració, però de forma independent, la gestió agrícola de l'aigua va reduir dràsticament el cabal d'entrada d'aigua dolça a la llacuna, provocant un canvi en el règim hídric. Es van analitzar els efectes a curt termini d'aquest canvi sobre la limnologia i el zooplàncton de la llacuna. Abans del canvi, la hidrologia era artificial ja que s'havia prolongat l'entrada d'aigua dolça d'acord amb la demanda agrícola, i per tant la llacuna presentava una elevada taxa de renovació de l'aigua i majors concentracions de nutrients. Després del canvi, la hidrologia va dependre més del clima, es van reduir les entrades d'aigua i es va allargar el període de confinament. La composició y dinàmica dels nutrients va tendir a assemblar-se a l'observada a les llacunes de la maresma, mentre que la comunitat del zooplàncton no ho va fer. L'estat ecològic de la llacuna va millorar després del canvi en el règim hídric.

Automatically constructing the semantic web

The storage and processing capacity realised by computing has lead to an explosion of data retention. We now reach the point of information overload and must begin to use computers to process more complex information. In particular, the proposition of the Semantic Web has given structure to this problem, but has yet realised practically. The largest of its problems is that of ontology construction; without a suitable automatic method most will have to be encoded by hand. In this paper we discus the current methods for semi and fully automatic construction and their current shortcomings. In particular we pay attention the application of ontologies to products and the particle application of the ontologies.

Responses of invertebrate trophic level, feeding guild and body size to the management of improved grassland field margins

P>1. Management of lowland mesotrophic grasslands in north-west Europe often makes use of inorganic fertilizers, high stocking densities and silage-based forage systems to maximize productivity. The impact of these practices has resulted in a simplification of the plant community combined with wide-scale declines in the species richness of grassland invertebrates. We aim to identify how field margin management can be used to promote invertebrate diversity across a suite of functionally diverse taxa (beetles, planthoppers, true bugs, butterflies, bumblebees and spiders). 2. Using an information theoretic approach we identify the impacts of management (cattle grazing, cutting and inorganic fertilizer) and plant community composition (forb species richness, grass species richness and sward architecture) on invertebrate species richness and body size. As many of these management practices are common to grassland systems throughout the world, understanding invertebrate responses to them is important for the maintenance of biodiversity. 3. Sward architecture was identified as the primary factor promoting increased species richness of both predatory and phytophagous trophic levels, as well as being positively correlated with mean body size. In all cases phytophagous invertebrate species richness was positively correlated with measures of plant species richness. 4. The direct effects of management practices appear to be comparatively weak, suggesting that their impacts are indirect and mediated though the continuous measures of plant community structure, such as sward architecture or plant species richness. 5. Synthesis and applications. By partitioning field margins from the remainder of the field, economically viable intensive grassland management can be combined with extensive management aimed at promoting native biodiversity. The absence of inorganic fertilizer, combined with a reduction in the intensity of both cutting and grazing regimes, promotes floral species richness and sward architectural complexity. By increasing sward architecture the total biomass of invertebrates also increased (by c. 60% across the range of sward architectural measures seen in this study), increasing food available for higher trophic levels, such as birds and mammals.

Intra-specific variation affects the structure of the natural enemy assemblage attacking pea aphid colonies

1. Intra-specific variation in plant defence traits has been shown to profoundly affect herbivore community structure. Here we describe two experiments designed to test whether similar effects occur at higher trophic levels, by studying pea aphid–natural enemy interactions in a disused pasture in southern England. 2. In the first experiment, the numbers and identity of natural enemies attacking different monoclonal pea aphid colonies were recorded in a series of assays throughout the period of pea aphid activity. 3. In the summer assay, there was a significant effect of clone on the numbers of aphidophagous hoverfly larvae and the total number of non-hoverfly natural enemies recruited. Clone also appeared to influence the attack rate suffered by the primary predator in the system, the hoverfly Episyrphus balteatus, by Diplazon laetatorius, an ichneumonid parasitoid. Colonies were generally driven to extinction by hoverfly attack, resulting in the recording of low numbers of parasitoids and entomopathogens, suggesting intense intra-guild predation. 4. To further examine the influence of clonal variation on the recruitment of natural enemies, a second experiment was performed to monitor the temporal dynamics of community development. Colonies were destructively sampled every other day and the numbers of natural enemies attacking aphid colonies were recorded. These data demonstrated that clonal variation influenced the timing, abundance, and identity of natural enemies attacking aphid colonies. 5. Taken together, these data suggest that clonal variation may have a significant influence on the patterns of interactions between aphids and their natural enemies, and that such effects are likely to affect our understanding of the ecology and biological control of these insect herbivores.

An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure

There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genotnes. Several statistical methods have been proposed to study the genetic structure using AFLP's but they assume Hardy-Weinberg equilibrium and do not estimate the inbreeding coefficient, F-IS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific F-IS and F-ST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.uif-grenoble.fi-/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.

PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

The effects of web logs and the semantic web on autonomous web agents

Search engines exploit the Web's hyperlink structure to help infer information content. The new phenomenon of personal Web logs, or 'blogs', encourage more extensive annotation of Web content. If their resulting link structures bias the Web crawling applications that search engines depend upon, there are implications for another form of annotation rapidly on the rise, the Semantic Web. We conducted a Web crawl of 160 000 pages in which the link structure of the Web is compared with that of several thousand blogs. Results show that the two link structures are significantly different. We analyse the differences and infer the likely effect upon the performance of existing and future Web agents. The Semantic Web offers new opportunities to navigate the Web, but Web agents should be designed to take advantage of the emerging link structures, or their effectiveness will diminish.

Using the web graph to influence application behaviour

The Web's link structure (termed the Web Graph) is a richly connected set of Web pages. Current applications use this graph for indexing and information retrieval purposes. In contrast the relationship between Web Graph and application is reversed by letting the structure of the Web Graph influence the behaviour of an application. Presents a novel Web crawling agent, AlienBot, the output of which is orthogonally coupled to the enemy generation strategy of a computer game. The Web Graph guides AlienBot, causing it to generate a stochastic process. Shows the effectiveness of such unorthodox coupling to both the playability of the game and the heuristics of the Web crawler. In addition, presents the results of the sample of Web pages collected by the crawling process. In particular, shows: how AlienBot was able to identify the power law inherent in the link structure of the Web; that 61.74 per cent of Web pages use some form of scripting technology; that the size of the Web can be estimated at just over 5.2 billion pages; and that less than 7 per cent of Web pages fully comply with some variant of (X)HTML.

The PSIPRED protein structure prediction server

The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.

A trophic cascade induced by predatory ants in a fig-fig wasp mutualism

Summary 1. A trophic cascade occurs when predators directly decrease the densities, or change the behaviour, of herbivores and thus indirectly increase plant productivity. The predator–herbivore– plant context is well known, but some predators attack species beneficial to plants (e.g. pollinators) and/or enemies of herbivores (e.g. parasites), and their role in the dynamics of mutualisms remains largely unexplored. 2. We surveyed the predatory ant species and studied predation by the dominant ant species, the weaver ant Oecophylla smaragdina, associated with the fig tree Ficus racemosa in southwest China. We then tested the effects of weaver ants on the oviposition behaviour of pollinating and non-pollinating fig wasps in an ant-exclusion experiment. The effects of weaver ants on fig wasp community structure and fig seed production were then compared between trees with and without O. smaragdina. 3. Oecophylla smaragdina captured more non-pollinating wasps (Platyneura mayri) than pollinators as the insects arrived to lay eggs. When ants were excluded, more non-pollinators laid eggs into figs and fewer pollinators entered figs. Furthermore, trees with O. smaragdina produced more pollinator offspring and fewer non-pollinator offspring, shifting the community structure significantly. In addition, F. racemosa produced significantly more seeds on trees inhabited by weaver ants. 4. Oecophylla smaragdina predation reverses the dominance of the two commonest wasp species at the egg-laying stage and favours the pollinators. This behavioural pattern is mirrored by wasp offspring production, with pollinators’ offspring dominating figs produced by trees inhabited by weaver ants, and offspring of the non-pollinator P. mayri most abundant in figs on trees inhabited by other ants. 5. Overall, our results suggest that predation by weaver ants limits the success of the non-pollinating P. mayri and therefore indirectly benefits the mutualism by increasing the reproductive success of both the pollinators and the plant. Predation is thus a key functional factor that can shape the community structure of a pollinator-plant mutualistic system. Key-words: competitive release, fig wasp, mutualism, predation, predator-exclusion experiment, trophic cascade

Fatty acids as trophic biomarkers in vitellogenic females in an impounded tropical river

Fatty acids have been used in marine biogeochemistry as food chain biomarkers, but in freshwater these studies are rare. In order to evaluate the fatty acid potential as biomarkers in freshwater, their profile was analyzed during vitellogenesis in two fish species, in both waterfall and reservoir environments of the Paraiba do Sul River Basin. Detrivorous Hypostomus affinis and omnivorous Geophagus brasiliensis seem to elongate and desaturate polyunsaturated fatty acids (PUFA) and transfer them to the ovaries` phospholipids. Waterfall Geophagus brasiliensis have more highly unsaturated fatty acids in the liver, but in the reservoir, accumulation mainly occurs in muscle and ovary triglycerides, suggesting trophic opportunism and a plasticity during vitellogenesis. In Hypostomus affinis, PUFA alteration occurs only in the reservoir, suggesting a high phytoplankton occurrence. Eutrophication and water speed is reflected in Hypostomus affinis ovaries by higher PUFAn3 and bacterial fatty acids. As in marine environments, analysis of mono- and polyunsaturated fatty acids during vitellogenesis can be used as a tool in food chain studies in freshwater.

Criteria for analysis of the structure of electronic scientific journals

This paper is the result of the Masters dissertation studying the role and history of scientific communication, especially the changes that have occurred after the appearance of electronic communication and computer networks. This study showed that hypertext systems are increasingly being used in the scientific and academic world in the production of electronic journals; this makes it possible for the user to rapidly access information in their area. However, these systems need to be improved to help the user during search and access to information. Both printed journals migrating to electronic media, and the exclusively electronic journals should present the current quality indicators. The attempt was made to discover whether characteristics related to printed journals are being maintained in their electronic counterparts. For this, a prototype model was developed to analyze the structure of electronic scientific journals; it composes 14 criteria expressing aspects of quality for these journals. It includes elements of Website Information Architecture and those already in place in printed scientific journals in order to ensure that basic functions - archiving and dissemination - are maintained in electronic publishing. Each criterion consists of variables, which measure the maintenance of these functions both in the migrating printed journals and the exclusively electronic ones. This prototype model was used to analyze Ciência da Informação On-line and DataGramaZero - Revista de Ciência da Informação. Results indicate that this model is able to find out if the basic functions of archiving and dissemination are being maintained in electronic journals. Therefore, its implementation is justified in electronic journals. The model can help librarians, authors, and users of electronic journals to identify quality journals, and assist editors in developing their projects. The material from the study may be included in the preservice and inservice education of Information Science professionals and to support editors of scientific journals.

Sistema de gerência de informação de processos industriais via Web

The structure of Industrial Automation bases on a hierarchical pyramid, where restricted information islands are created. Those information islands are characterized by systems where hardware and software used are proprietors. In other words, they are supplied for just a manufacturer, doing with that customer is entailed to that supplier. That solution causes great damages to companies. Once the connection and integration with other equipments, that are not of own supplier, it is very complicated. Several times it is impossible of being accomplished, because of high cost of solution or for technical incompatibility. This work consists to specify and to implement the visualization module via Web of GERINF. GERINF is a FINEP/CTPetro project that has the objective of developing a software for information management in industrial processes. GERINF is divided in three modules: visualization via Web, compress and storage and communication module. Are presented results of the utilization of a proposed system to information management of a Natural Gas collected Unit of Guamar´e on the PETROBRAS UN-RNCE.

Foraging by the omnivorous crab Pachygrapsus transversus affects the structure of assemblages on sub-tropical rocky shores

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)