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.

The development of a wind tunnel DAQ system by using Labview tools

This paper presents the experimental three-year learning activity developed by a group of teachers in a wind tunnel facility. The authors, leading a team of students, carried out a project consisting of the design, assembly and testing of a wind tunnel. The project included all stages of the process from its initial specifications to its final quality flow assessments, going through the calculation of each element, and the building of the whole wind tunnel. The group of (final year) students was responsible for the whole wind tunnel project as a part of their bachelor degree project. The paper focuses on the development of wind tunnel data acquisition software. This automatic tool is essential to improve the automation of the data acquisition of the wind tunnel facility systems, in particular for a 6DOF multi-axis force/torque sensor. This work can be considered as a typical example of real engineering practice: a set of specifications that has to be modified due to the constraints imposed throughout the project, in order to obtain the final result

Peer Assessment and Self-assessment: Effective Learning Tools in Higher Education.

When used appropriately, self- and peer-assessment are very effective learning tools. In the present work, instructor formative assessment and feedback, self-assessment (SA), and peer-assessment (PA) have been compared. During the first part of a semester, the students followed a continuous formative assessment. Subsequently, they were divided into two subgroups based on similar performances. One subgroup performed SAs, and the other followedPAduring the last part of the course. The performances of the two groups in solving problems were compared. Results suggest that PA is a more effective learning tool than SA, and both are more effective than instructor formative assessment. However, a survey that was conducted at the end of the experiment showed higher student confidence in instructor assessment than in PA. The students recognized the usefulness of acting as peer assessors, but believed that SA helped them more than PA.

Tools for mixed-criticality partitioned systems: partitioning algorithm and extensibility support

The development of mixed-criticality virtualized multicore systems poses new challenges that are being subject of active research work. There is an additional complexity: it is now required to identify a set of partitions, and allocate applications to partitions. In this job, a number of issues have to be considered, such as the criticality level of the application, security and dependability requirements, operating system used by the application, time requirements granularity, specific hardware needs, etc. MultiPARTES [6] toolset relies on Model Driven Engineering (MDE) [12], which is a suitable approach in this setting. In this paper, it is described the support provided for automatic system partitioning generation and toolset extensibility.

Functional genomics tools to decipher the pathogenicity mechanisms of the necrotrophic fungus Plectosphaerella cucumerina in Arabidopsis thaliana

The analysis of the interaction between Arabidopsis thaliana and adapted (PcBMM) and nonadapted (Pc2127) isolates of the necrotrophic fungus Plectosphaerella cucumerina has contributed to the identification of molecular mechanisms controlling plant resistance to necrotrophs.To characterize the pathogenicity bases of the virulence of necrotrophic fungi in Arabidopsis, we developed P. cucumerina functional genomics tools using Agrobacterium tumefaciens-mediated transformation.We generated PcBMM-GFP and Pc2127-GFP transformants constitutively expressing the green fluorescence protein (GFP), and a collection of random T-DNA insertional PcBMM transformants. Confocal microscopy analyses of the initial stages of PcBMM-GFP infection revealed that this pathogen, like other necrotrophic fungi, does not form an appressorium or penetrate into plant cells, but causes successive degradation of leaf cell layers

The optimal allocation rule and the water market as the most effective tools of managing water shortage in an irrigation district

The conference program will cover all areas of environmental and resource economics, ranging from topics prevailing in the general debate, such as climate change, energy sources, water management and ecosystem services evaluation, to more specialized subjects such as biodiversity conservation or persistent organic pollutants. The congress will be held on the Faculty of Economics of the University of Girona, located in Montilivi, a city quarter situated just few minutes from the city center, conveniently connected by bus lines L8 and L11.

Testing of Android testing tools: development of a benchmark for the evaluation

With the ever growing trend of smart phones and tablets, Android is becoming more and more popular everyday. With more than one billion active users i to date, Android is the leading technology in smart phone arena. In addition to that, Android also runs on Android TV, Android smart watches and cars. Therefore, in recent years, Android applications have become one of the major development sectors in software industry. As of mid 2013, the number of published applications on Google Play had exceeded one million and the cumulative number of downloads was more than 50 billionii. A 2013 survey also revealed that 71% of the mobile application developers work on developing Android applicationsiii. Considering this size of Android applications, it is quite evident that people rely on these applications on a daily basis for the completion of simple tasks like keeping track of weather to rather complex tasks like managing one’s bank accounts. Hence, like every other kind of code, Android code also needs to be verified in order to work properly and achieve a certain confidence level. Because of the gigantic size of the number of applications, it becomes really hard to manually test Android applications specially when it has to be verified for various versions of the OS and also, various device configurations such as different screen sizes and different hardware availability. Hence, recently there has been a lot of work on developing different testing methods for Android applications in Computer Science fraternity. The model of Android attracts researchers because of its open source nature. It makes the whole research model more streamlined when the code for both, application and the platform are readily available to analyze. And hence, there has been a great deal of research in testing and static analysis of Android applications. A great deal of this research has been focused on the input test generation for Android applications. Hence, there are a several testing tools available now, which focus on automatic generation of test cases for Android applications. These tools differ with one another on the basis of their strategies and heuristics used for this generation of test cases. But there is still very little work done on the comparison of these testing tools and the strategies they use. Recently, some research work has been carried outiv in this regard that compared the performance of various available tools with respect to their respective code coverage, fault detection, ability to work on multiple platforms and their ease of use. It was done, by running these tools on a total of 60 real world Android applications. The results of this research showed that although effective, these strategies being used by the tools, also face limitations and hence, have room for improvement. The purpose of this thesis is to extend this research into a more specific and attribute-­‐ oriented way. Attributes refer to the tasks that can be completed using the Android platform. It can be anything ranging from a basic system call for receiving an SMS to more complex tasks like sending the user to another application from the current one. The idea is to develop a benchmark for Android testing tools, which is based on the performance related to these attributes. This will allow the comparison of these tools with respect to these attributes. For example, if there is an application that plays some audio file, will the testing tool be able to generate a test input that will warrant the execution of this audio file? Using multiple applications using different attributes, it can be visualized that which testing tool is more useful for which kinds of attributes. In this thesis, it was decided that 9 attributes covering the basic nature of tasks, will be targeted for the assessment of three testing tools. Later this can be done for much more attributes to compare even more testing tools. The aim of this work is to show that this approach is effective and can be used on a much larger scale. One of the flagship features of this work, which also differentiates it with the previous work, is that the applications used, are all specially made for this research. The reason for doing that is to analyze just that specific attribute in isolation, which the application is focused on, and not allow the tool to get bottlenecked by something trivial, which is not the main attribute under testing. This means 9 applications, each focused on one specific attribute. The main contributions of this thesis are: A summary of the three existing testing tools and their respective techniques for automatic test input generation of Android Applications. • A detailed study of the usage of these testing tools using the 9 applications specially designed and developed for this study. • The analysis of the obtained results of the study carried out. And a comparison of the performance of the selected tools.

Papyrus, EATOP, and MetaEdit+: a comparison between the EAST-ADL modeling tools

Several Architecture Description Languages (ADLs) are emerging as models to describe and represent system architectures. Among others, EAST-ADL language is highlighted. It represents an abstraction of embedded software systems for automobiles. Given the need to implement the EAST-ADL language, there are many modeling tools to perform this task. The scope of this thesis is a detailed comparison of three EAST-ADL editors: Papyrus, EATOP and MetaEdit +, providing a conceptual framework, describing the comparison criteria, and finally exemplifying thanks to the Brake-By-Wire use case which has been provided, and whose development is not the subject of this project. The motivation for developing this project is to provide comparison guide between these three modeling tools to facilitate developers choice when deciding the tool in which develop their work. RESUMEN. Diversos Lenguajes de Descripción de Arquitecturas (ADLs) están surgiendo como modelos para describir y representar arquitecturas de sistemas. Entre ellos es destacado el lenguaje EAST-ADL, que representa una abstracción de los sistemas de software embebido para automóviles. Ante la necesidad de implementar el lenguaje EAST-ADL, han surgido diversas herramientas de modelado que llevan a cabo esta tarea. El alcance de este proyecto consiste en una comparación detallada de tres editores EAST-ADL: Papyrus, EATOP y MetaEdit+, proporcionando un marco conceptual, describiendo los criterios de comparación y finalmente ejemplificando con el caso de uso Brake-By-Wire que nos ha sido proporcionado, y cuyo desarrollo no es sujeto de este proyecto. La motivación para desarrollar este proyecto parte de proporcionar al usuario una guía comparativa de estas tres herramientas de modelado para facilitar su elección a la hora de desarrollar su trabajo.