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- PublicationAccès libreDetection and characterization of exogenous DNA – from genetically modified organisms (GMOs) to naturally admixed genomes(Neuchâtel : Université de Neuchâtel, 2025)Cette thèse porte sur la détection de l’ADN exogène, qu’il provienne naturellement par métissage ou qu’il soit introduit par modification génétique, en développant des méthodes permettant d’identifier ces traces génétiques. Au Chapitre 1, nous avons développé un test de séquençage d’amplicons hautement multiplexé pour détecter les OGM de première génération. Nos tests utilisent une plateforme de microfluidique et le séquençage de nouvelle génération (NGS) pour amplifier en parallèle et séquencer plusieurs cibles OGM. Nous avons conçu 230 paires d’amorces pour amplifier des événements de modification génétique dans différentes cultures. Nous avons également inclus des marqueurs de codage-barres pour l’identification des espèces. Nous avons démontré que notre test peut détecter les OGM de première génération par amplification parallèle. Notre test a également révélé des événements OGM « inconnus » que les tests PCR standards pourraient ne pas détecter. Étant donné sa capacité à traiter simultanément plusieurs cibles et échantillons, notre méthode basée sur la microfluidique peut servir d’outil de dépistage initial. Elle permet une détection large qui peut ensuite être examinée à l’aide de méthodes de confirmation plus sensibles. Au Chapitre 2, nous avons présenté LOCO (algorithme de COpy à faible profondeur), un nouveau modèle computationnel permettant d’inférer l’ascendance locale à partir de données de séquençage à faible couverture, sans dépendre de panels de référence externes. LOCO s’appuie sur des modèles de type Li & Stephens, mais construit ses haplotypes de référence directement à partir des données. À travers des simulations, nous avons démontré que LOCO peut inférer correctement l’ascendance dans des génomes issus d’admixture et détecter de longues introgressions. Toutefois, nous avons observé que les segments courts d’ascendance sont souvent mal attribués, une limitation fréquente des outils d’inférence d’ascendance locale. Au Chapitre 3, nous avons appliqué cette approche d’inférence d’ascendance à la détection d’OGM de seconde génération. Nous avons simulé, dans ce cadre, une modification de type OGM de seconde génération dans des génomes de riz, en copiant artificiellement de petits segments d’un individu à un autre. En principe, LOCO devrait identifier ces segments comme des introgressions s’ils diffèrent du fond d’ascendance de l’individu. Toutefois, nous avons rencontré des difficultés à initialiser les paramètres nécessaires au bon fonctionnement de LOCO. Étant donné que l’ensemble des paramètres requis est inconnu pour cet ensemble de données, LOCO n’a pas réussi à trouver les solutions de maximum global. Il est donc nécessaire de développer une meilleure stratégie d’initialisation des paramètres pour les données réelles, car dans la pratique, la vraie valeur de ces paramètres est rarement connue. Dans l’ensemble, cette thèse démontre que nos méthodes de séquençage et nos outils computationnels peuvent considérablement améliorer la détection de l’ADN exogène. ABSTRACT This thesis focuses on detecting exogenous DNA, whether it arises naturally through admixture or is introduced through genetic modification, by advancing methods for identifying these genetic traces. In Chapter 1, we developed a highly multiplexed amplicon sequencing assay to detect first-generation GMOs. Our assays use a microfluidics platform and next-generation sequencing (NGS) to amplify in parallel and sequence multiple GMO targets. We designed 230 primer pairs to amplify GM events across different crops. We also included barcoding markers for species identification. We demonstrated that our assay can detect first-geneation GMOs in a parallel amplification. Our assay also uncovered potential “unknown” GM events that standard PCR screens might miss. Given its scalability in simultaneously processing multiple targets and samples, our microfluidics-based assay can serve as a first-pass screening tool. It enables broad detection that can be reviewed with confirmatory methods. In Chapter 2, we introduced LOCO (LOw depth COpy algorithm), a new computational model to infer local ancestry from low-coverage sequencing data without depending on external reference panels. LOCO builds upon Li & Stephens–style copy models but constructs its reference haplotypes directly from the data. By simulation tests, we demostrated that LOCO can infer the correct ancestry in admixed genomes and detect longer introgressions. However, we observed that short ancestry segments are often misassigned, a common limitation of local-ancestry tools. In Chapter 3, we applied this ancestry-inference idea to second-generation GMO detection. Here, we simulated second-generation GMO-like modification in rice genomes by artificially copying small segments from one individual into another. In principle, LOCO should flag these segments as introgression if they are different from the individual’s ancestry background. However, we encountered difficulties with initialising the parameters needed by LOCO. Given that the set of parameters used by LOCO are unknown for this data set, LOCO failed to find the global maxima solutions. We need a better strategy for initialising the parameters from real-world data bceause we rarely know the true value of the parameters. Overall, this thesis demonstrates thats our sequencing and computational methods can significantly improve the detection of exogeneus DNA.
- PublicationAccès libre
- PublicationAccès libreLearning by doing: Intercultural lessons from a transnational course(2025)According to Dervin (2010), intercultural communication entails savoir-faire, savoir-analyser but also savoir-(ré)agir, in other words identifying actions in co-constructed discourses, being able to analyse discourses in terms of stereotypes, and being able to adapt one’s emotions and actions in intercultural settings. Acting and learning by doing thus play an important role in developing intercultural competencies. We strongly believe that students need to be challenged to act in multicultural settings and that is why we set up a transnational course jointly taught by three teachers from three European universities (Åbo Akademi University in Turku, Finland; University of West Bohemia in Plzen, Czech Republic; University of Neuchâtel, Switzerland). The goal of the course was to work in small international and multidisciplinary groups and to identify a sustainability challenge (within the framework of the UN sustainable development goals), define and investigate the challenge, as well as create and present a feasible solution, following the design sprint methodology . In this article, we want to analyse the pilot of this course and question how intercultural communication was presented to students, through self-assessment questionnaires and tasks and how it was enacted by students in small group discussions, debates and decision-making processes. Our main goal was to offer minimal guidance and to focus on the savoir-(ré)agir that the students would experience in their group work. To assess our approach, we rely on students’ and teachers’ reflective evaluations of the course and we will base our analysis on teachers’ logs, student interviews at the end of the course, students’ learning journals and two surveys filled in by students at the beginning of the course and the end. This will allow us to map an eventual change in students’ perspectives. With this protocol we wish to explore how much students need to be guided to develop their intercultural communication competence.
- PublicationAccès libreStability, Reciprocity, and Antecedent-Outcome Relations of Different Job Crafting Forms(2025)Job crafting involves employees proactively changing their jobs to better suit their preferences. Recent integrative frameworks organize the multifaceted construct with superordinate factors, emphasizing the distinction between behavioral (actions to change job characteristics) and cognitive crafting (reframing one’s view on the job). However, most existing job crafting literature focuses on behavioral crafting, leaving the dynamics between behavioral and cognitive crafting and their comparability regarding antecedents and outcomes unclear. This study provides a systematic juxtaposition of behavioral and cognitive crafting forms over time, examining their stability, reciprocal influences, and their unique relations with decision-making autonomy as an antecedent and person-job fit as an outcome. It also distinguishes between approach (enlarging one’s roles) and avoidance (reducing one’s roles) strategies within each form. Using structural equation modeling within a longitudinal design across three measurement points (N = 284 German employees, time lag of four weeks each), our study revealed remarkably high levels of stability in all job crafting forms. Unexpectedly, we found no support for reciprocal relationships between the crafting forms over time nor longitudinal relations with decision-making autonomy and person-job fit. In an additional latent profile analysis, we identified four distinct job crafting profiles with significant variations in used job crafting forms and their associations with person-job fit, providing further insights into the construct's interplay. Our findings seem to question the generalizability of common theoretical assumptions in the field and emphasize the importance of investigating more differentiated mechanisms of individual job crafting forms in the future.