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Detection of genetically modified organisms using highly multiplexed amplicon sequencing
No full textThe circulation of products based on genetically modified (GM) organisms is highly regulated by some governments with strict implementation rules for the breeding, planting, marketing, labelling, and trading of such products. To ensure compliance, accurate detection methods for GM events are necessary, along with assurance that GM material falls within relevant threshold levels. The increasing complexity and potential of undocumented GM are a growing challenge for genetic screening. Here, we developed and assessed a highly multiplexed amplicon sequencing assay for the detection of GM events based on a microfluidics platform and next-generation sequencing (NGS). To probe GM events comprehensively, we designed a total of 230 new amplicons to cover flanking, promoter, junction, and coding sequences of GM sequences. In addition, we designed and implemented parallel amplification of ribosomal and chloroplast markers to define crop species identity from potentially mixed samples. Using reference GM material of 11 crop species and multiple amplicons, we successfully detected the presence of 10 known modifications per GM event. We also find that reported flanking sequences of GM events may not be all useful for diagnostic. We assessed the assay's potential to detect GM events in mixed samples as well as in highly diluted DNA. Finally, we performed a prospective search of potentially undocumented GM events in plant material. Our microfluidics-based amplicon GM detection approach fills important gaps in detecting potentially undocumented and complex GM events by recovering a wide range of specific amplicon sequences for evaluation. Integrating highly parallel amplicon assays in GM screening efforts should be an effective complement to aid post-market monitoring and regulatory compliance efforts
Attention, tu veux tomber ! La périphrase verbale vouloir + VINF à valeur de futur proche : panorama diasystémique
No full textLa périphrase verbale ‹vouloir+Vinf› pour exprimer l’ultériorité existe depuis l'ancien français, en compétition avec ‹aller+Vinf›. Cette construction, basée sur des concepts cognitifs universels (aussi présents, entre autres, en anglais et en roumain), survit jusqu’à nos jours, avec des valeurs qui varient selon les régions. Dans cette étude, l'évolution diachronique, l'extension dans les parlers galloromans et les usages contemporains en français sont examinés, avec des données récentes recueillies via la méthode du crowdsourcing. Les résultats d’une analyse portant sur les réponses obtenues auprès de témoins francs-comtois et suisses romands, et évaluant les variables influençant cette construction (personne verbale, modalité, effet lexical), permettent de montrer que la tournure dans son emploi le moins syntaxiquement contraint n’est aujourd’hui guère employée en dehors du Jura franco-suisse, du moins en Europe.tru
Linking musical metaphors, emotions and feelings of entrainment evoked by electronic music: From the physical properties of sounds to the experience of listening to music
Get PDFThis paper proposes a perspective on the experience of listening to music, where sounds are conceived as objects of auditory perception in interaction with the listener’s body. This interaction in considered to be a continuous process of attributing meaning by the listener, based on the possibility of action in accordance to the music; to possibility to move to – or to be moved by – the music, both metaphorically and literally. Musical meaning is, here, understood in terms of metaphors and emotions. In this paper, the relationships between metaphors and emotions are analyzed from the perspective of embodied (music) cognition, which considers the body as central for cognitive (musical) processing. The phenomena of the body synchronizing to the music, as a consequence of it’s interaction with it, is referred to as rhythmic entrainment (Trost et al., 2017). Within this theoretical framework, an enactivist standpoint affirms that action tendencies are intertwined with perception. According to such, physical (acoustic) properties of sounds are cognitively mapped through sensorimotor (bodily) representations: a process of attributing musical meaning to the interaction between the listener with the music. Listening to music necessarily implies processing sequences of sounds through time, often conceptualized in terms of metaphors of (bodily) motion – embodied musical meaning (Johnson, 1997). The motion of music through time is considered to be understood by the listener in terms of how this motion is reflected as motion in the body, whether though overt movements (as dancing) or covert sensations (as introspective emotions). Describing the experience of listening to music in terms of metaphorical and emotional language sheds light on how bodily motion is associated with musical motion, through the process of attribution of embodied musical meaning.
The core of this paper is based on an empirical study conducted with the aim to explore interactions between the physical (acoustic) properties of sounds and the experience of listening to music. By doing so, this study also aims to provide a scientific contribution to an embodied (music) cognition framework. Two categories of electronic music (ambient and dance) were considered as inclined to exert rather sedative or stimulative effects on the body of the listener. The study was composed of three phases, and combines tools from Computational Sciences and Music Psychology. The first phase consisted in the extraction and analyses of a set of acoustic features with the MIR toolbox (Lartillot & Toiviainen, 2007), from 16 electronic music excerpts (length of 30 seconds). In the second phase, 172 participants evaluated the music through an online survey. They rated items of the Geneva Musical Metaphors Scale (GEMMES) (Schaerlaeken et al., 2019), to assess musical metaphors, of the Geneva Emotional Music Scale (GEMS) (Zenter et al., 2008), and the two-dimensional emotional model of valance and arousal (Russel, 1980), to assess musical emotions, and of the Musical Entrainment Questionnaire (MEQ) (Labbé & Grandjean, 2014), to assess subjective feelings of entrainment. In both phases, data was analyzed with Principal Component Analysis (PCA), to obtain a few relevant groups of variables based on the correlations between them. The third phase consisted in computing linear mixed-effects models, in order to explore the interaction between the physical properties of music (acoustic features) and the experience of listening to music (survey ratings). Finally, results of all three phases were compared with those from a similar study on classical music (Schaerlaeken et al., 2022).
The first phase resulted in in two principal components of acoustic features; two groups of mathematical descriptors of sound-waves associated with perceptual characteristics of music. Dance music was associated with high timbre (in terms of frequency spectrum and energy), simple rhythms and regular structure, while the opposite was true for ambient music. The comparison with classical music indicated that acoustic features related to timbre and rhythm are core descriptors, independently of genre, whereas those related to structure/dynamics were particularly relevant only for electronic music.
The second phase also resulted two principal components, to describe the participant’s evaluations of the music. Dance music was most represented by elements associated with overt motion (i.e. body movements): metaphors of “Movement” and “Force”, emotions of “Power”, “Joyful Activation” and “Tension”, as well as arousal and feelings of entrainment. On the other hand, ambient music was most represented by elements associated with to covert motion (i.e. internal body sensations): metaphors of “Wandering”, “Flow” and “Interior”, emotions of “Wonder”, “Ten-
derness”, “Peacefulness”, “Nostalgia”, “Sadness” and “Transcendence”. This supports an understanding of embodied music cognition, where the differences between dance and ambient electronic music mirror the differences between stimulative and sedative influences of music on the body of the listener. Furthermore, the two groups of correlations were consistent with the results found with classical music, suggesting similarities in how meaning is attributed to the music through embodied experiences of motion.
The third phase showed that acoustic features associated with the perception of timbre, rhythm and structure influence how ambient and dance music are evaluated by the listeners. As a general trend, higher frequency spectrum and more regular structure was correlated with higher ratings of overt motion elements. However, specific trends also apply to each category of electronic music. Ambient music was rated higher for covert motion and lower for overt motion in excerpts with lower energy, irregular structure and complex rhythm. For dance music, the peak of highest ratings for overt motion and lowest for covert motion in excerpts with moderate energy, regular structure and simple rhythm. Ratings for overt motion decrease and those for covert motion increase, if energy is too high, structure too regular and rhythm too simple. This pattern is not the reciprocal of the one found for ambient music. This may be a reflection of the importance of violations of musical expectations as a major component of musical meaning (Meyer, 1956). In this sense, dance music would have more potential to induce action, if containing a balanced degree of complexity and irregularity. Otherwise, the music becomes too predictable and the listener feels less inclined to move.
By exploring the link between acoustic features of sound and subjective evaluation of music, this study contributes to bridging the gap between MIR technology and music psychology (Acounturier & Bigand, 2013; Siedenburg et al., 2016). The choice of electronic music is also of scientific interest in itself, as it is a rapidly expanding contemporary genre of music, which is only marginally addressed in scientific research, in comparison to classical music for instance. Furthermore, the study contributes to a framework of embodied music cognition framework in two ways. First and foremost, the results are consistent with those of Schaerlaeken et al. (2022), linking feelings of entrainment with specific metaphors and emotions into two main clusters which broadly represent two modes of bodily interaction with the music (overt and covert motion). This study explores a different genre of music (electronic), and as such reinforces their ecological validity. Secondly, the conceptual framework mobilized to interpret the results provides tools to consider the role of the body in the construal of musical meaning. An enactivist perspective of cognition adequately accounts for differences between categories of electronic music (ambient and dance), with respects to diverging tendencies of action that the music can afford to the listener.
The degree to which the results of the study are generalizable depends mainly on two limitations. Firstly, all participants to the online survey belonged to WEIRD (Western-Educated-Industrialized-Rich-Democratic) population samples (Apicella, Norenzayan & Henrich, 2020). Considering the culturally-dependent nature of metaphors (Dancygier & Sweetser, 2014; Nuñez & Cooperrider, 2006; Zbikowski, 2008) and of emotions (Le Breton, 2021), the results cannot be generalized outide of WEIRD population. Secondly, the sample size of the music selection was relatively small (16 excerpts) and the range of different styles of music was limited and relatively polarized (ambient vs. dance). For the conclusions to be more robust, similar studies would have to be replicated with a wider variety and diversity of music.
The study, with it’s strengths and limitations, enlightens a few orientations for further research. The first points towards bridging the gap between MIR technology and music psychology, by promoting cross-disciplinary research and applications. It would be relevant for research in music psychology to explore different methodologies of MIR analysis, which are currently used to categorize large databases of music (Aucouturier & Pachet, 2003; Chen, 2014; Defferrand et al., 2016; Diakopoulos, 2009; Kirss, 2007; Lefaivre & Zhang, 2018; Nie, 2022). This approach would greatly benefit also from the integration of perceptual features (Aljanaki & Soleymani; 2018), as they provide a good mediator between the physical (acoustic) properties of sounds and the psychological phenomenology of listening to music. The second orientation refers to laboratory research. It would be relevant to investigate the neural correlates of rhythmic entrainment and action-perception coupling, while participants passively listen to music. This can be investigated by collecting EEG data of mu waves over the motor-related brain areas (Anderson, 2020; Fox et al., 2016; Hari, 2006; Pineda, 2005; Ross, 2022; Wu et al., 2016). This could further be integrated with physiological data (Bartlett, 1996; Gaston, 1951; Hodges, 2016; Matyja, 2016), in order to establish correlations between neural, physiological and subjective entrainment as well as emotional reactions. In addition, motion caption studies can be designed to further explore motor entrainment and specific movements associated with dancing to different styles of music (Toiviainen & Carlson, 2022). Finally, these previous orientations could be combined with ethnographical fieldwork in a fundamentally inter-disciplinary approach. This would imply contextually-situated qualitative research, based on the observation and analysis of individual movements and social interactions during live music performances. Unlike in a laboratory setting, this could shed light on phenomena social entrainment (Garcia, 2020; Witek, 2019). A mixed approach, able to integrate laboratory-based and fieldwork-based methodologies, would contribute to a holistic understanding of the experience of listening to music, from a perceptual, physiological, motor and social integrated perspective. Furthermore, intercultural studies could additionally shed light on universal vs. cultural aspects of music cognition. Bottom-up methodologies, similar to those involved in the creation of the GEMS and GEMMES, can be used to establish cross-cultural comparisons in musically-relevant metaphorical and emotional labels.
These opportunities for future scientific research also reflect potential societal applications. Firstly, it contributes to the inclusion of perceptual and cognitive aspects in the classification of music. Music providers which deal with large databases of music could improve their services by adopting concepts as metaphors, emotions and entrainment in complement of a classification methodology purely based on acoustic features of sound. Music psychology has the potential to provide insight where MIR technology finds its limitations. Secondly, music composition and performance can surely benefit from a better understanding of how meaning is conveyed through music, and the role of the body in this process. Metaphorical and emotional concepts can aid musicians to better comprehend their own intentions of expression through music and how to do so through with, and through their bodies. Similarly, such aspects can also have a positive influence in the field of music education. Metaphorical and emotional language is useful to transmit knowledge and insight from the teacher to the student
Usage-Based Approaches to Germanic Languages
Get PDFThe theoretical outlook of usage-based linguistics is a position that views language as a dynamic, evolving system and that recognizes the importance of usage frequency and frequency effects in language, as well as the foundational role of domain-general sociocognitive processes. Methodologically, usage-based studies draw on corpus-linguistic methods, experimentation, and computational modeling, often in ways that combine different methods and triangulate the results. Given the availability of corpus resources and the availability of experimental participants, there is a rich literature of usage-based studies focusing on Germanic languages, which at the same time has greatly benefited from usage-based research into other language families. This research has uncovered frequency effects based on measurements of token frequency, type frequency, collocational strength, and dispersion. These frequency effects result from the repeated experience of linguistic units such as words, collocations, morphological patterns, and syntactic constructions, which impact language production, language processing, and language change. Usage-based linguistics further investigates how the properties of linguistic structures can be explained in terms of cognitive and social processes that are not in themselves linguistic. Domain-general sociocognitive processes such as categorization, joint attention, pattern recognition, and intention reading manifest themselves in language processing and production, as well as in the structure of linguistic units. In addition to research that addresses the form and meaning of such linguistic units at different levels of linguistic organization, domains of inquiry that are in the current focus of usage-based studies include linguistic variation, first and second-language acquisition, bilingualism, and language change
Popular Culture, Identity and Creativity across the Afro-European matrix
Get PDFThis article draws on ethnographic elements collected in the heterogeneous field of African music and dance in France and French-speaking Switzerland, as well as on a previous literature on popular travelling music and dance genres between African and European cities. It participates in an ongoing conversation about the concept of the Black Mediterranean, and insists on its relevance to analyse migrations, cross-cultural formations and postcolonial conversations taking place between some European countries and their former colonies through popular music and dance productions. Ethnography and history of travelling music and dance genres leads to approach the Black Mediterranean as both a borderland of racial violence and inequalities, and a web of cultural signs, transactions, and practices that connect the African continent and European cities. This transcontinental matrix participates in reconfiguring the representations of Africanity, Blackness and Afropeanity in ambiguous and multifaceted ways.tru
À l’épreuve de l’école à la maison. Expériences et vécu de l’enseignement à distance durant le semi-confinement lié à la pandémie de la Covid-19 pour les élèves issu-e-s de la migration dans le canton de Vaud
Get PDFL’enseignement à distance durant le semi-confinement lié à la pandémie de la Covid-19 en Suisse a bouleversé les modes d’apprentissage et d’enseignement. Les élèves issu-e-s de la migration, particulièrement sujet-te-s aux inégalités scolaires, ont fortement été impacté-e-s par la fermeture des écoles. Ce travail de mémoire propose de mettre en lumière les expériences et le vécu de l’enseignement à distance des élèves issu-e-s de la migration dans le canton de Vaud, tout en s’intéressant au rôle que les différent-e-s acteur-ice-s du système scolaire (enseignant-e-s et parents) ont exercé durant cette période. Pour ce faire, dix entretiens semi-directifs ont été réalisés avec 5 élèves issu-e-s de la migration, 4 enseignant-e-s et un parent, toutes et tous domicilié-e-s dans le canton de Vaud. Les résultats ont montré que les élèves issu-e-s de la migration sont des acteur-ice-s rationnel-le-s et que leur investissement scolaire a été influencé par l’arrêt des évaluations certificatives ainsi que par le manque de soutien scolaire de la part des parents et du corps enseignant. Cette absence de soutien familial est en partie due à la méconnaissance du système scolaire suisse, au manque de capital culturel et à la continuité des activités professionnelles. De plus, le manque de consignes claires quant à l’application de la continuité pédagogique a créé des différences dans les méthodes d’enseignement à distance. Enfin, la disparité de ressources financières allouées aux écoles entre les communes « riches » et « pauvres » provoque des différences dans les conditions d’apprentissage et dans la qualité de l’enseignement. Ces éléments, corrélés à un modèle mixte d’orientation des élèves très peu hétérogène et à la ségrégation spatiale perpétuée par les écoles, renforcent les inégalités scolaires existantes dans le canton de Vaud
Unraveling the microbial matrix : high-resolution profiling of synergistic and antagonistic forces shaping the crop microbiome
No full textInstitut de biologie, th. no 3128
Jury composé de :
Prof. Daniel Croll, directeur de thèse, UniNE
Prof. Pilar Junier, UniNE
Dr. Viviane Cordovez, Netherlands Institute of Ecology, Pays-Bas
Prof. Monika Maurhofer, ETH ZürichPlants host diverse yet taxonomically structured communities of microorganisms. These microorganisms colonize every accessible plant tissue, influencing both plant growth and health. There is substantial interest to exploit beneficial members of plant microbiomes for new sustainable management strategies in crop production. However, our understanding of these interactions in field conditions, particularly at the species and strain level, is still limited. Moreover, microbial pathogens can rapidly adapt to changing environments such as the application of pesticides or host resistance. This thesis offers a comprehensive perspective on the genetic mechanisms of pathogen adaptation and the dynamics of microbial communities in crop plants, providing a high-resolution view of strain-specific microbial interactions that shape plant health.
Mapping microbial genomic variation at the strain level in environmental samples has posed a significant challenge in the field. This thesis addresses this challenge through two interconnected and complementary approaches. The first approach involves wholegenome sequencing and comprehensive structural variant analysis of a large fungal pathogen population to detect genomic signatures indicative of recent adaptation. We examined how Rhynchosporium commune, a major fungal pathogen of barley, has adapted to the host environment and fungicide applications. We screened the genomes of 125 isolates from diverse global populations and identified 7879 gene duplications and 116 gene deletions, primarily resulting from segmental chromosomal duplications. While Copy Number Variations (CNVs) are usually under negative selection, we observed that genes impacted by CNVs are overrepresented in functions related to host exploitation, such as effectors and cell wall-degrading enzymes. We conducted genome-wide association studies (GWAS) and identified a large segmental duplication of the Cytochrome P450 Family 51 gene (CYP51A) that contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We demonstrated that the adaptive CNVs were likely created by recently active transposable element families. Furthermore, we found that specific transposable element families are significant drivers of recent gene copy-number variation. Collectively, these findings demonstrate how extensive segmental duplications provide the raw material for recent adaptation in global populations of a fungal pathogen.
The second method leverages whole-genome sequences to construct pangenomes, facilitating the creation of taxon-specific amplicons. These amplicons allow us to monitor strain diversity in the field and to build co-occurrence networks that reveal synergistic and antagonistic interactions between strains. Specifically, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons. We focused on the wheat microbiome as a proof-ofprinciple and achieved unprecedented resolution for the wheat-associated Pseudomonas microbiome and the ubiquitous fungal pathogen Zymoseptoria tritici. We achieved more than a three-fold increase in phylogenetic resolution compared to existing ribosomal amplicons. The designed amplicons accurately capture species and strain diversity, ii outperforming full-length 16S and Internally Transcribed Spacer (ITS) amplicons. To broaden the utility of our approach, we generated pangenome-informed amplicon templates for additional key bacterial and fungal genera.
Pangenome-informed microbiome profiling allows tracking of microbial community dynamics in complex environments and overcomes limitations in phylogenetic resolution. We then used this approach to track microbial communities in the wheat phyllosphere across time and space, detecting fine-grained species and strain-specific dynamics. Our findings reveal a high level of strain-specificity in Pseudomonas interactions, both within and between kingdoms. Through systematic analysis of negative interactions, we discovered a consortium of ten taxa that potentially suppress seven fungal pathogens. We confirmed the strain-specific interactions of Pseudomonas with different strains of the major fungal pathogen Z. tritici using co-inoculation experiments involving Pseudomonas strains and Z. tritici isolates from the same field. Consistent with our prediction, we identified a Pseudomonas poae isolate as the most antagonistic towards Z. tritici. Overall, we demonstrate the potential of taxon-specific high-resolution network inference in studying microbial interaction networks. We highlight how understanding species and strain-specific dynamics can inform the development of effective biocontrol strategies
Private money and money market integration: the role of payments infrastructure in 19th century Switzerland
No full textUsing newly collected discount rate data for six Swiss cities, we find no evidence of increasing integration during a 30-year period of lightly regulated free banking. We attribute this to two structural issues: banks had incentives to protect their local monopolies, and the inherent instability of free banking meant that there was always a risk (which varied across banks) of a bank run. We use a novel counterfactual to show that these risks increased discount rate dispersion, and argue that as a result, public regulation of payments infrastructure was necessary for money market integration