Molecular tools to improve chestnut management: El Bierzo as a case study

The European chestnut (Castanea sativa Mill.) is a multipurpose species that has been widely cultivated around the Mediterranean basin since ancient times. New varieties were brought to the Iberian Peninsula during the Roman Empire, which coexist since then with native populations that survived the last glaciation. The relevance of chestnut cultivation has being steadily growing since the Middle Ages, until the rural decline of the past century put a stop to this trend. Forest fires and diseases were also major factors. Chestnut cultivation is gaining momentum again due to its economic (wood, fruits) and ecologic relevance, and represents currently an important asset in many rural areas of Europe. In this Thesis we apply different molecular tools to help improve current management strategies. For this study we have chosen El Bierzo (Castile and Leon, NW Spain), which has a centenary tradition of chestnut cultivation and management, and also presents several unique features from a genetic perspective (next paragraph). Moreover, its nuts are widely appreciated in Spain and abroad for their organoleptic properties. We have focused our experimental work on two major problems faced by breeders and the industry: the lack of a fine-grained genetic characterization and the need for new strategies to control blight disease. To characterize with sufficient detail the genetic diversity and structure of El Bierzo orchards, we analyzed DNA from 169 trees grafted for nut production covering the entire region. We also analyzed 62 nuts from all traditional varieties. El Bierzo constitutes an outstanding scenario to study chestnut genetics and the influence of human management because: (i) it is located at one extreme of the distribution area; (ii) it is a major glacial refuge for the native species; (iii) it has a long tradition of human management (since Roman times, at least); and (iv) its geographical setting ensures an unusual degree of genetic isolation. Thirteen microsatellite markers provided enough informativeness and discrimination power to genotype at the individual level. Together with an unexpected level of genetic variability, we found evidence of genetic structure, with three major gene pools giving rise to the current population. High levels of genetic differentiation between groups supported this organization. Interestingly, genetic structure does not match with spatial boundaries, suggesting that the exchange of material and cultivation practices have strongly influenced natural gene flow. The microsatellite markers selected for this study were also used to classify a set of 62 samples belonging to all traditional varieties. We identified several cases of synonymies and homonymies, evidencing the need to substitute traditional classification systems with new tools for genetic profiling. Management and conservation strategies should also benefit from these tools. The avenue of high-throughput sequencing technologies, combined with the development of bioinformatics tools, have paved the way to study transcriptomes without the need for a reference genome. We took advantage of RNA sequencing and de novo assembly tools to determine the transcriptional landscape of chestnut in response to blight disease. In addition, we have selected a set of candidate genes with high potential for developing resistant varieties via genetic engineering. Our results evidenced a deep transcriptional reprogramming upon fungal infection. The plant hormones ET and JA appear to orchestrate the defensive response. Interestingly, our results also suggest a role for auxins in modulating such response. Many transcription factors were identified in this work that interact with promoters of genes involved in disease resistance. Among these genes, we have conducted a functional characterization of a two major thaumatin-like proteins (TLP) that belongs to the PR5 family. Two genes encoding chestnut cotyledon TLPs have been previously characterized, termed CsTL1 and CsTL2. We substantiate here their protective role against blight disease for the first time, including in silico, in vitro and in vivo evidence. The synergy between TLPs and other antifungal proteins, particularly endo-p-1,3-glucanases, bolsters their interest for future control strategies based on biotechnological approaches.

Methodology for estimating building integrated photovoltaics electricity production under shadowing conditions and case study

Building integrated photovoltaic (BIPV) systems are a relevant application of photovoltaics. In countries belonging to the International Energy Agency countries, 24% of total installed PV power corresponds to BIPV systems. Electricity losses caused by shadows over the PV generator have a significant impact on the performance of BIPV systems, being the major source of electricity losses. This paper presents a methodology to estimate electricity produced by BIPV systems which incorporates a model for shading losses. The proposed methodology has been validated on a one year study with real data from two similar PV systems placed on the south façade of a building belonging to the Technical University of Madrid. This study has covered all weather conditions: clear, partially overcast and fully overcast sky. Results of this study are shown at different time scales, resulting that the errors committed by the best performing model are below 1% and 3% in annual and daily electricity estimation. The use of models which account for the reduced performance at low irradiance levels also improves the estimation of generated electricity.

Building resilience to water scarcity in Southern Spain: A case study of rice farming in Doñana protected wetlands

Agricultural water management needs to evolve in view of increased water scarcity, especially when farming and natural protected areas are closely linked. In the study site of Don?ana (southern Spain), water is shared by rice producers and a world heritage biodiversity ecosystem. Our aim is to contribute to defining adaptation strategies that may build resilience to increasing water scarcity and minimize water conflicts among agricultural and natural systems. The analytical framework links a participatory process with quantitative methods to prioritize the adaptation options. Bottom-up proposed adaptation measures are evaluated by a multi-criteria analysis (MCA) that includes both socioeconomic criteria and criteria of the ecosystem services affected by the adaptation options. Criteria weights are estimated by three different methods?analytic hierarchy process, Likert scale and equal weights?that are then compared. Finally, scores from an MCA are input into an optimization model used to determine the optimal land-use distribution in order to maximize utility and land-use diversification according to different scenarios of funds and water availability. While our results show a spectrum of perceptions of priorities among stakeholders, there is one overriding theme that is to define a way to restore part of the rice fields to natural wetlands. These results hold true under the current climate scenario and evenmore so under an increased water scarcity scenario.

Structuring research methods and data with the research object model: genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as “which particular data was input to a particular workflow to test a particular hypothesis?”, and “which particular conclusions were drawn from a particular workflow?”. Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.

Social tags and linked data for ontology development: a case study in the financial domain

We describe a domain ontology development approach that extracts domain terms from folksonomies and enrich them with data and vocabularies from the Linked Open Data cloud. As a result, we obtain lightweight domain ontologies that combine the emergent knowledge of social tagging systems with formal knowledge from Ontologies. In order to illustrate the feasibility of our approach, we have produced an ontology in the financial domain from tags available in Delicious, using DBpedia, OpenCyc and UMBEL as additional knowledge sources.

Capacity Building through education, research and collaboration: AFRICA BUILD, an eHealth Case Study

AFRICA BUILD (AB) is a Coordination Action project under the 7th European Framework Programme having the aim of improving the capacities for health research and education in Africa through Information and Communication Technologies (ICT). This project, started in 2012, has promoted health research, education and evidence-based practice in Africa through the creation of centers of excellence, by using ICT,?know-how?, eLearning and knowledge sharing, through Web-enabled virtual communities.

Using the Cross-Entropy Method for Control Optimization: A Case Study of See-and-Avoid on Unmanned Aerial Vehicles

This paper presents an adaptation of the Cross-Entropy (CE) method to optimize fuzzy logic controllers. The CE is a recently developed optimization method based on a general Monte-Carlo approach to combinatorial and continuous multi-extremal optimization and importance sampling. This work shows the application of this optimization method to optimize the inputs gains, the location and size of the different membership functions' sets of each variable, as well as the weight of each rule from the rule's base of a fuzzy logic controller (FLC). The control system approach presented in this work was designed to command the orientation of an unmanned aerial vehicle (UAV) to modify its trajectory for avoiding collisions. An onboard looking forward camera was used to sense the environment of the UAV. The information extracted by the image processing algorithm is the only input of the fuzzy control approach to avoid the collision with a predefined object. Real tests with a quadrotor have been done to corroborate the improved behavior of the optimized controllers at different stages of the optimization process.

A small settings case study using TSPi in a software project

This article introduces a small setting case study about the benefits of using TSPi in a software project. An adapted process from the current process based on the TSPi was defined. The pilot project had schedule and budget constraints. The process began by gathering historical data from previous projects in order to get a measurement repository. The project was launched with the following goals: increase the productivity, reduce the test time and improve the product quality. Finally, the results were analysed and the goals were verified

Food market analysis: a case study of the Glocal methodology in the Dominican Republic

The present paper provides an insight into the food value chain of three specific sectors (fruit and vegetables, poultry and rice) in the Dominican Republic. The Glocal methodology used for the study combines a global view with local conditions and thus it can be applied to food markets. Each of these food chains is analyzed by following traditional industrial organization theory, based on structure, conduct and performance. Regarding the specific case of the Dominican Republic, different sources of information are used to analyze the weaknesses of the studied chains, including direct interviews. The food value chains of fruit and vegetables, poultry and rice in the Dominican Republic show a lack of structure and they are undergoing changes; however, they also have great opportunities to improve efficiency by making some changes.

El programa Case Study House: industria, propaganda y vivienda

En enero de 1945, John Entenza, editor de la revista californiana Arts & Architecture , puso en marcha el programa Case Study House, un ambicioso proyecto cuyo firme objetivo era investigar las posibilidades y soluciones del problema de la vivien - da al que se enfrentaba los Estados Unidos de la posguerra. Para ello, Entenza diseñó una novedosa estrategia de colaboración entre algunos de los mejores arquitectos californianos del momento y la maquinaria industrial estadounidense, abierta a un proceso de reconversión de producción bélica a objetos para la población civil que tendría lugar en un tiempo récord. Así, el artículo propone el análisis de esa relación entre empresa y domesticidad, entre viabilidad económica y calidad arquitectónica, entre procesos de prefabricación y espíritu individual. Todos ellos conceptos aparentemente opuestos pero que, de la mano del programa Case Study House, lograron un entendimiento que a día de hoy sigue resultando extraordinario.

Automatic segmentation of rivers as a tool for assessing river responses. Case study: the Porma and Curueño rivers, nw Spain.

Automatic segmentation using univariate and multivariate techniques provides more objective and efficient segmentations of the river systems (Alber & Piégay, 2011) and can be complementary to the expert criteria traditionally used (Brenden et al., 2008) INTEREST: A powerful tool to objectively segment the continuity of rivers, which is required for diagnosing problems associated to human impacts OBJECTIVE: To evaluate the potentiality of univariate and multivariate methods in the assessment of river adjustments produced by flow regulation

Discourses and values underpin public debate on fracking in Spain: a case study at the crossroad

In the EU context extraction of shale and oil gas by hydraulic fracturing (fracking) differs from country to country in terms of legislation and implementation. While fossil fuel extraction using this technology is currently taking place in the UK, Germany and France have adopted respective moratoria. In between is the Spanish case, where hydrocarbon extraction projects through fracking have to undergo mandatory and routine environmental assessment in accordance with the last changes to environmental regulations. Nowadays Spain is at the crossroad with respect to the future of this technology. We presume a social conflictt in our country since the position and strategy of the involved and confronted social actors -national, regional and local authorities, energy companies, scientists, NGO and other social organization- are going to play key and likely divergent roles in its industrial implementation and public acceptance. In order to improve knowledge on how to address these controverted situations from the own engineering context, the affiliated units from the Higher Technical School of Mines and Energy Engineering at UPM have been working on a transversal program to teach values and ethics. Over the past seven years, this pioneering experience has shown the usefulness of applying a consequentialist ethics, based on a case-by-case approach and costs-benefits analysis both for action and inaction. As a result of this initiative a theoretical concept has arisen and crystallized in this field: it is named Inter-ethics. This theoretical perspective can be very helpful in complex situations, with multi-stakeholders and plurality of interests, when ethical management requires the interaction between the respective ethics of each group; professional ethics of a single group is not enough. Under this inter-ethics theoretical framework and applying content analysis techniques, this paper explores the articulation of the discourse in favour and against fracking technology and its underlying values as manifested in the Spanish traditional mass media and emerging social media such as Youtube. Results show that Spanish public discourse on fracking technology includes the costs-benefits analysis to communicate how natural resources from local communities may be affected by these facilities due to environmental, health and economic consequences. Furthermore, this technology is represented as a solution to the "demand of energy" according to the optimistic discourse while, from a pessimistic view, fracking is often framed as a source "environmental problems" and even natural disasters as possible earthquakes. In this latter case, this negative representation could have been influenced by the closure of a macro project to store injected natural gas in the Mediterranean Sea using the old facilities of an oil exploitation in Amposta (Proyecto Cástor). The closure of this project was due to the occurrence of earthquakes whose intensity was higher than the originally expected by the experts in the assessment stage of the project.