DoMoRe – A recommender system for domain modeling

Domain modeling is an important activity in early phases of software projects to achieve a shared understanding of the problem field among project participants. Domain models describe concepts and relations of respective application fields using a modeling language and domain-specific terms. Detailed knowledge of the domain as well as expertise in model-driven development is required for software engineers to create these models. This paper describes DoMoRe, a system for automated modeling recommendations to support the domain modeling process. We describe an approach in which modeling benefits from formalized knowledge sources and information extraction from text. The system incorporates a large network of semantically related terms built from natural language data sets integrated with mediator-based knowledge base querying in a single recommender system to provide context-sensitive suggestions of model elements

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity

Resistance mechanisms to Verticillium wilt are well studied in tomato, cotton and Arabidopsis, but much less in legume plants. Because legume plants establish nitrogen-fixing symbioses in their roots, resistance to root-attacking pathogens merits particular attention. The interaction between the soil-borne pathogen Verticillium alfalfae and the model legume Medicago truncatula was investigated using a resistant (A17) and a susceptible (F83005.5) line. As shown by histological analyses, colonization by the pathogen was initiated similarly in both lines. Later on, the resistant line A17 eliminated the fungus, whereas the susceptible F83005.5 became heavily colonized. Resistance in line A17 does not involve homologs of the well-characterized tomato Ve1 and V. dahliae Ave1 genes. A transcriptomic study of early root responses during initial colonization (i.e. until 24 h post-inoculation) similarly was performed. Compared to the susceptible line, line A17 displayed already a significantly higher basal expression of defense-related genes prior to inoculation, and responded to infection with up-regulation of only a small number of genes. Although fungal colonization was still low at this stage, the susceptible line F83005.5 exhibited a disorganized response involving a large number of genes from different functional classes. The involvement of distinct phytohormone signaling pathways in resistance as suggested by gene expression patterns was supported by experiments with plant hormone pretreatment before fungal inoculation.Gene co-expression network analysis highlighted five main modules in the resistant line, whereas no structured gene expression was found in the susceptible line. One module was particularly associated to the inoculation response in A17. It contains the majority of differentially expressed genes, genes associated with PAMP perception and hormone signaling, and transcription factors. An in silico analysis showed that a high number of these genes also respond to other soil-borne pathogens in M. truncatula, suggesting a core of transcriptional response to root pathogens. Taken together, the results suggest that resistance in M. truncatula line A17 might be due to innate immunity combining preformed defense and PAMP-triggered defense mechanisms, and putative involvement of abscisic acid

Characterisation of sunflower root colonisation by Phoma macdonaldii

Phoma macdonaldii, the causal agent of black stem disease of sunflower (Helianthus annuus), also attacks roots and collars of the plants, resulting in early death. Totally resistant lines do not exist for infection of the aerial parts, but tolerant lines have been characterised. This paper presents a study on colonisation of a partially resistant and a susceptible sunflower line by P. macdonaldii. The fungus was transformed with a constitutively expressed reporter gene encoding the jellyfish green fluorescent protein via Agrobacterium tumefaciens, and colonisation of sunflower roots by this transformed strain was studied by various microscopy techniques including confocal and scanning electron microscopy. The results show that penetration of the fungus into the root occurred through natural fissures or through the epidermis and was similar in both lines. In contrast, the colonisation rate of the stele was reduced in the partially resistant line, and the morphology of the fungal hyphae was also affected. The effect on hyphal morphology was strongest in the stele, indicating a localised production of defence compounds in this line

First report of Colletotrichum gloeosporioides on citrus in Algeria

Wither-tip symptoms of twigs were observed on cultivated sweet orange and lemon trees in Algeria. The causal agent was identified as Colletotrichum gloeosporioides on the basis of cultural and morphological features. The identification of the fungus was confirmed by sequencing of the internal transcribed spacer region of rDNA. Pathogenicity tests revealed that C. gloeosporioides isolated from withered twigs caused typical anthracnose symptoms on orange leaves. This is the first report on Colletotrichum gloeosporioides as causal agent of anthracnose in Citrus trees in Algeria

Unterstützung von Domänenmodellierung durch automatisierten Wissenserwerb und Modellierungsempfehlungen

Domain modeling is an important model-driven engineering activity, which is typically used in the early stages of software projects. Domain models capture concepts and relationships of respective application fields using a modeling language and domain-specific terms. They are a key factor in achieving shared understanding of the problem area among stakeholders, improving communication in software development, and generating code and software. Domain models are a prerequisite for domain-specific language development and are often implemented in software and data integration and software modernization projects, which constitute the larger part of industrial IT investment. Several studies from recent years have shown that model-driven methods are much more widespread in the industry than previously thought, yet their application is challenging. Creating domain models requires that software engineers have both experience in model-driven engineering and detailed domain knowledge. While the former is one of the general modeling skills, the required domain knowledge varies from project to project. Domain knowledge acquisition is a time-consuming manual process because it requires multidisciplinary collaboration and gathering of information from different groups of people, documents, and other sources of knowledge, and is rarely supported in current modeling environments. Consistent access to large amounts of structured domain knowledge is not possible due to the heterogeneity of formats, access methods, schemas, and semantic representations. Besides, existing suitable knowledge bases were mostly manually created and are therefore not extensive enough. The automated construction of knowledge resources utilizes mainly information extraction approaches that focus on factual knowledge at the instance level and therefore cannot be used for conceptual-level domain modeling. This thesis develops novel methods and tools that provide domain information directly during modeling to reduce the initial effort of using domain modeling and to help software developers create domain models. It works on the connection of the areas of software modeling, knowledge bases, information extraction and recommender systems to automatically acquire conceptual knowledge from structured knowledge sources and unstructured natural language datasets, to transform the aggregated knowledge into appropriate recommendations, and to develop suitable assistance services for modeling environments. With this thesis, the paradigm of Semantic Modeling Support is proposed, the methodological foundation for providing automated modeling assistance. It includes an iterative procedure of model refinement, knowledge acquisition, and element recommendation that allows to query and provide the necessary domain knowledge for a range of support scenarios at each stage of domain model development, keeping the human in the loop. To address the lack of conceptual knowledge resources, new methods are developed to extract conceptual terms and relationships directly from large N-gram text data using syntactic patterns, co-occurrences, and statistical features of text corpora. A large Semantic Network of Related Terms is automatically constructed with nearly 6 million unique one-word terms and multi-word expressions connected with over 355 million weighted binary and ternary relationships. It allows to directly answer top-N queries. This thesis introduces an extensible query component with a set of fully connected knowledge bases to uniformly access structured knowledge with well-defined relationships. The developed Mediator-Based Querying Architecture with Generic Templates is responsible for retrieving lexical information from heterogeneous knowledge bases and mapping to modeling language-specific concepts. Furthermore, it is demonstrated how to implement the semantic modeling support strategies by extending the widely used Eclipse Modeling Project. The Domain Modeling Recommender System generates context-sensitive modeling suggestions based on the connected knowledge bases, the semantic network of terms, and an integrated ranking strategy. Finally, this thesis reports on practical experience with the application of the developed methods and tools in three research projects.Domänenmodellierung ist eine wichtige Methode der modellgetriebenen Softwareentwicklung, die oftmals in den frühen Phasen von Softwareprojekten verwendet wird. Domänenmodelle erfassen Konzepte und Beziehungen des jeweiligen Anwendungsgebietes unter Verwendung einer Modellierungssprache und domänenspezifischer Begriffe. Sie sind ein Schlüsselfaktor für ein gemeinsames Verständnis des Problembereichs unter den Projektbeteiligten, für die Verbesserung der Kommunikation während der Softwareentwicklung und für die Generierung von Code und Software. Domänenmodelle sind eine Voraussetzung für die Entwicklung von domänenspezifischen Sprachen und werden häufig bei Softwaremodernisierung sowie bei Software- und Datenintegrationsprojekten eingesetzt, die den größten Teil der industriellen IT-Investitionen ausmachen. Mehrere Studien aus den letzten Jahren haben gezeigt, dass modellgetriebene Methoden in der Branche verbreiteter sind, als bisher angenommen, ihre Anwendung jedoch eine Herausforderung darstellt. Das Erstellen von Domänenmodellen setzt voraus, dass Softwareentwickler sowohl über Erfahrung in der modellgetriebenen Softwareentwicklung als auch über detaillierte Domänenkenntnisse verfügen. Ersteres gehört zu allgemeinen Modellierungskompetenzen, jedoch variiert das erforderliche Domänenwissen von Projekt zu Projekt. Der Erwerb von Domänenwissen ist ein zeitaufwendiger manueller Prozess, da er interdisziplinäre Zusammenarbeit und Informationsbeschaffung von verschiedenen Personengruppen, Dokumenten und anderen Wissensquellen erfordert und in aktuellen Modellierungsumgebungen kaum unterstützt wird. Ein einheitlicher Zugriff auf große Mengen von strukturiertem Domänenwissen ist aufgrund der Heterogenität von Formaten, Zugriffsmethoden, Schemata und semantischen Repräsentationen nicht möglich. Außerdem wurden vorhandene geeignete Wissensbasen meist manuell erstellt und sind daher nicht umfangreich genug. Bei der automatisierten Erstellung von Wissensressourcen werden hauptsächlich Ansätze der Informationsextraktion verwendet, die Faktenwissen auf Instanzebene erschließen und daher nicht für Domänenmodellierung auf Konzeptebene geeignet sind. In dieser Arbeit werden neuartige Methoden und Tools entwickelt, die Domäneninformationen direkt während der Modellierung bereitstellen, um den anfänglichen Aufwand der Domänenmodellierung zu verringern und Softwareentwicklern bei der Erstellung von Domänenmodellen zu helfen. Sie befasst sich mit der Verknüpfung der Bereiche Softwaremodellierung, Wissensdatenbanken, Informationsextraktion und Empfehlungssysteme, um automatisch konzeptionelles Wissen aus strukturierten Datenquellen und unstrukturierten natürlichsprachlichen Texten zu erschließen, um das aggregierte Wissen in geeignete Empfehlungen zu transformieren, und um geignete Unterstützungsdienste für Modellierungswerkzeuge zu entwickeln. Diese Dissertation führt die Semantische Modellierungsunterstützung, die methodische Grundlage für eine automatisierte Modellierungshilfe, ein. Sie umfasst ein iteratives Verfahren der Modellverfeinerung, Wissensbeschaffung und Elementempfehlung, welches das erforderliche Domänenwissen für eine Reihe von Unterstützungsszenarien in jeder Phase der Domänenmodellentwicklung abfragt und bereitstellt. Das Fehlen von konzeptionellen Wissensressourcen wird durch die Entwicklung neuer Methoden adressiert, die konzeptionelle Begriffe und Beziehungen direkt aus großen N-Gram Textdaten mit Hilfe von syntaktischen Mustern, Kookkurrenzen und statistischen Merkmalen großer Textkorpora extrahieren. Es wird ein großes Semantisches Netz verwandter Begriffe mit fast 6 Millionen Ein- und Mehrwortbegriffen automatisch konstruiert, die mit über 355 Millionen gewichteten binären und ternären Beziehungen verbunden sind, wodurch Top-N-Anfragen direkt beantwortet werden können. Die Dissertation führt eine erweiterbare Abfragekomponente mit einer Reihe fertig verbundener Wissensbasen ein, um einheitlich auf strukturiertes Wissen mit spezifischen Relationen zuzugreifen. Die entwickelte Mediator-basierte Abfragearchitektur mit generischen Templates fragt automatisch lexikalische Informationen aus heterogenen Wissensbasen ab und ordnet sie Modellierungssprachkonzepten zu. Außerdem wird gezeigt, wie die Strategien der semantischen Modellierungsunterstützung implementiert werden, indem das weit verbreitete Eclipse Modeling Project erweitert wird. Das Domänenmodellierungsempfehlungssystem generiert kontextsensitive Modellierungsvorschläge, basierend auf den verbundenen Wissensbasen, dem semantischen Begriffsnetz und einer integrierten Ranking-Strategie. Schließlich berichtet diese Arbeit über praktische Erfahrungen bei der Anwendung der entwickelten Methoden und Werkzeuge in drei Forschungsprojekten

Contrôle génétique et biodiversité de la tolérance à Verticillium albo-atrum chez Medicago

La verticilliose est une maladie vasculaire des plantes dont les symptômes typiques sont un flétrissement des parties aériennes, des feuilles chlorosées puis séchées, et dans les cas de maladie grave la mort de la plante. Au niveau des racines on observe une coloration brune du tissu conducteur. Cette maladie est causée par un champignon du sol du genre Verticillium. Les espèces majeures V. dahliae et V. albo-atrum sont responsables de pertes importantes de rendement sur de nombreuses cultures. Le champignon entre dans la racine par des blessures ou par des fissures au niveau de sites d émergence de racines latérales, puis il avance vers le cylindre central et envahit les vaisseaux du xylème. Sa croissance reste pendant longtemps limitée aux vaisseaux qu il colonise en avançant vers les parties aériennes de la plante. Aux stades tardifs, le champignon sort du cylindre central et colonise les autres tissus. En Europe, V. albo-atrum constitue l une des principales causes de maladies chez la luzerne pérenne et est à l origine de pertes économiques très importantes. La capacité de V. albo-atrum de survivre dans le sol ainsi que sa localisation protégée dans le cylindre centrale des plantes infectées en font un pathogène difficile à combattre, la lutte génétique par sélection de variétés tolérantes apparaissant comme une approche prometteuse. Cependant, la capacité des microorganismes pathogènes de s adapter rapidement à des nouvelles plantes hôtes est une menace bien connue de la durabilité des variétés résistantes. Au laboratoire, des travaux ultérieurs ont établi que la plante modèle des légumineuses Medicago truncatula, une espèce sauvage proche de la luzerne cultivée, peut être utilisée pour étudier les mécanismes de résistance et sensibilité vis-à-vis de V. alboatrum. Une lignée résistant et une lignée sensible ont été identifiées et l étude de la descendance d un croisement entre ces deux lignées a permis d identifier un locus majeur (Quantitative trait locus, QTL) contrôlant la résistance à une souche de V. albo-atrum isolée de la Luzerne (Ben et al., 2013 ; Negahi en 6e co-auteur). Ce travail a également montré qu il existait une grande biodiversité au sein de l espèce M. truncatula par rapport à la réponse à cette souche de V. albo-atrum.Verticillium wilt, caused by Verticillium albo-atrum (Vaa) and Verticillium dahliae (Vd), is responsible for yield losses in many economically important crops. The capacity of pathogenic fungi to adapt to new hosts is a well-known threat to the durability of resistant crop varieties. Medicago truncatula is a good model for studying resistance and susceptibility to Verticillium wilt in legume plants. Phenotyping a population of inbred lines from a cross between resistant parent line A17 and susceptible parent F83005.5 contributed to the identification of a first QTL controlling resistance to an alfalfa strain of Vaa in M. truncatula. Then, 25 M. truncatula genotypes from a core collection and six Vaa and Vd strains were used to study the potential of non-host Verticillium strains isolated from different plant species to infect this legume plant, and the plant s susceptibility to the pathogens. The experiment was arranged as factorial based on a randomized complete block design with three replications. The wilt symptoms caused by Vaa and Vd were scored on a disease index scale from 0 to 4, during 30 days after inoculation of ten day-old plantlets. Disease severity was quantified by the parameters Maximum Symptom Scores (MSS) and Areas Under the Disease Progress Curves (AUDPC). Highly significant differences were observed among plant genotypes and fungal strains, and their interaction was also significant. The correlation between MSS and AUDPC was 0.86 and highly significant. The most severe symptoms were caused by the alfalfa strain Vaa-V31-2 and the least severe by Vd-JR2, as shown by mean values obtained on the 25 genotypes. M. truncatula genotype TN8.3 was identified as the most susceptible genotype by mean values obtained with the 6 fungal strains, whereas F11013-3, F83005.9 and DZA45.6 were highly resistant to all strains studied. The results were used to choose parents for studying the genetics of resistance in M. truncatula to a nonalfalfa Verticillium strain. So, in the second part of this work, genotype A17 which was susceptible and genotype F83005.5 which was resistant to the potato strain Vaa-LPP0323 and recombinant inbred lines (RILs) from a cross between these genotypes were selected in order to study the genetic control of resistance to this strain of the pathogen. Our experimental design was a randomized complete blocks with 116 RILs and three replications. High genetic variability and transgressive segregation for resistance to Vaa-LPP0323 were observed among RILs. A total of four QTLs controlling resistance to Vaa-LPP0323 were detected for the parameters MSS and AUDPC. The phenotypic variance explained by each QTL (R2) was moderate, ranging from 3 to 21%. A negative sign of additive gene effects showed that favourable alleles for resistance come from the resistant parent.TOULOUSE-INP (315552154) / SudocSudocFranceF

Étude de l'interaction de Medicago truncatula avec Fusarium oxysporum et du rôle de l'acide salicylique dans les interactions de la plante avec différents agents pathogènes et symbiotiques

Des études de l'interaction de la plante modèle des légumineuses Medicago truncatula avec des microorganismes pathogènes et symbiotiques ont été réalisées. Tout d'abord un pathosystème fongique a été caractérisé: M. truncatula en interaction avec Fusarium oxysporum spp., champignon responsable des fusarioses, soit du flétrissement vasculaire ou de la pourriture racinaire chez de nombreuses plantes cultivées. Deux lignées de M. truncatula: A17 et F83005.5 ont été identifiées comme sensible et tolérante respectivement à F. oxysporum f.sp. medicaginis, la forma specialis attribuée à la luzerne. De plus 9 souches de F. oxysporum isolées de différentes plantes hôtes et une souche non pathogène du sol ont été testées dans des expériences d'inoculation avec ces deux lignées. Elles ont toutes été capables d'induire les symptômes de la maladie chez M. truncatula. A l'aide d'une souche de F. oxysporum f.sp. medicaginis exprimant le gène rapporteur GFP, les étapes de colonisation de la racine par le champignon ont été caractérisées. Les observations en microscopie à fluorescence et microscopie confocale des racines d'A17 et F83005.5 ont indiqué un patron de colonisation inhabituel et ont montré que la tolérance de F83005.5 n'était pas corrélée à un mécanisme d'exclusion du cylindre central. Cependant, des différences dans l'expression de gènes de défense ont été détectées entre les deux lignées. Dans la deuxième partie, le rôle de l'acide salicylique a été étudié. Les résultats d'expériences avec l'acide salicylique exogène ont indiqué que le prétraitement de racines avec ce composé pouvait conférer une protection aux plantes vis-à-vis de F. oxysporum f.sp. medicaginis et la bactérie phytopathogène Ralstonia solanacearum. Avec l'objectif d'étudier le rôle de l'acide salicylique endogène dans les interactions avec les microorganismes, la transformation génétique de M. truncatula avec le gène NahG codant le salicylate hydroxylase a été entreprise. Cette enzyme dégrade l'acide salicylique en catechol. Seulement la lignée 2HA a pu être transformée et régénérée en plantes transgéniques. Ces plantes 2HA-NahG ont été inoculées avec des microorganismes pathogènes (R. solanacearum, Verticillium albo-atrum, F. oxysporum f. sp. medicaginis Colletotrichum trifolii et C. higginsianum) ainsi qu'avec le champignon endomycorhizien Glomus intraradices. Les limitations expérimentales n'ont pas permis de conclure définitivement, mais indiquent qu'il est possible que la signalisation par l'acide salicylique ne soit pas impliquée dans les défenses de M. truncatula face à ces microorganismes pathogènes et symbiotiques.A study on the interactions of the plant model legume Medicago truncatula (M.t.) with pathogens and symbiotic microorganisms was undertaken. First, a fungal pathosystem was characterized: M. truncatula in interaction with Fusarium oxysporum spp., the causal agent of Fusariosis, of Fusarium wilt and of root rot in many crop plants. Two M. truncatula lines, A17 and F83005.5, were identified as susceptible and tolerant respectively to F. oxysporum f.sp. medicaginis, the forma specialis related to alfalfa. Besides, 9 strains of F. oxysporum isolated from different host plants and a non-pathogenic soil-borne strain were tested in inoculation experiments with both lines. All the strains were able to trigger disease symptoms in M. truncatula. Using the F. oxysporum f.sp. medicaginis strain transformed with the GFP reporter gene, the stages of the root colonization by the fungi were characterized. Fluorescence and confocal microscopy observations on A17 and F83005.5 roots showed an unusual pattern of colonization and showed that the F83005.5 tolerance was not related to an exclusion mechanism in the central cylinder. However, differences on defence gene expression were detected in both lines. In the second part, the role of salicylic acid was studied. Results of experiments with exogenous salicylic acid indicated that prior treatment of roots with this compound may confer a protection towards F. oxysporum f. sp. medicaginis and the phytopathogenic bacterium Ralstonia solanacearum. With the goal to study the role of endogenous salicylic acid, the genetic transformation of M. truncatula with the NahG gene was initiated. This gene codes for a salicylate hydroxylase which degrades salicylic acid to catechol. Only the highly embryogenic 2HA line could be transformed and regenerated into transgenic plants. These 2HA plants were inoculated with pathogenic microorganisms (Ralstonia solanacearum, Verticillium albo-atrum, Fusarium oxysporum f.sp. medicaginis Colletotrichum trifolii and C. higginsianum) as well as the mycorrhiza fungus Glomus intraradices. Experimental limitations did not allow us to conclude definitely, but it seems possible that the salicylic acid signaling way may not be implicated in the defence of M. truncatula against these pathogenic and symbiotic microorganismsTOULOUSE-INP (315552154) / SudocSudocFranceF