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Opgaven voor de regionale arbeidsmarkt 2023-2027

Plants have a dynamic immune system to protect themselves against pathogens. Recognition of a pathogen leads to the activation of this immune system, steered by different phytohormones. One of these, salicylic acid, regulates plant responses to biotrophic pathogens that thrive on living host tissue. Typical SA-mediated responses are the production of antimicrobial proteins and metabolites and the strengthening of the cell wall. These responses can occur both locally and systemically. Due to their nature, these responses cost energy and resources that cannot be invested in plant growth and development. This suppression also works the other way around: active growth and developmental processes suppress immunity. This mutual inhibition is called the growth-immunity tradeoff and is actively regulated by the plant. The research in this thesis is focused on the model plant Arabidopsis thaliana (thale cress), in which the SA content is controlled at the level of synthesis and catabolism. Two enzymes that catabolize SA through hydroxylation are the paralogous 2-oxoglutarate Fe(II)-dependent oxygenases DMR6/S5H (DOWNY MILDEW RESISTANT 6/SA 5-HYDROXYLASE) and DLO1/S3H (DMR6-LIKE OXYGENASE 1/SA 3-HYDROXYLASE). dmr6/dlo1 mutants have enhanced SA levels and therefore a constitutively active immune system and enhanced disease resistance. The high SA levels of double mutant plants cause hyperresistance but also dwarfism. On the other hand, overexpression of DMR6 or DLO1 leads to depletion of SA and thus enhanced susceptibility. We use the perturbed SA catabolism of the dmr6/dlo1 mutants and DMR6/DLO1 overexpression lines to investigate the SA-mediated growth-immunity tradeoff. We found that altered expression of DMR6 and/or DLO1 had major effects on the transcriptome that correlated to the plant’s SA content. We found that enhanced SA levels in dmr6/dlo1 mutants caused reduced photosynthetic efficiency and a sped up development and reduced SA levels in DMR6/DLO1 overexpression lines led to reduced pathogen-associated molecular pattern (PAMP)-triggered immune responses. We further identified a significant effect of the genetic background to perturbations in DMR6/DLO1 expression in different Arabidopsis accessions: several Arabidopsis accessions had a reduced growth tradeoff but retained high disease resistance. To systematically investigate the genetics behind regulation of the growth-immunity tradeoff, we further employed a forward genetics screen for restored growth and high resistance in dmr6-3 dlo1 double mutants and identified seven unique zund mutants. These plants carried mutations in known regulators of SA synthesis (ICS1, ISOCHORISMATE SYNTHASE 1), perception (NPR1, NONEXPRESSOR OF PR GENES 1), or signaling (PAD4, PHYTOALEXIN DEFICIENT 4), indicating that a suppression of SA synthesis or SA responses reduces the growth tradeoff in high immunity dmr6-3 dlo1 mutants. Three other zund mutants carried a mutation in the same gene: MED15a (MEDIATOR 15a), a component of the MEDIATOR complex for transcription initiation. We investigate the function of MED15a in the growth-immunity tradeoff in detail, and find that around 80% of dmr6-3 dlo1-induced gene expression changes are genetically dependent on the integrity of two amino acids in the MED15a kinase-inducible (KIX) domain. I discuss the implications of this research for applications to breed for sustainable disease resistance in crops.

Plants have a dynamic immune system to protect themselves against pathogens. Recognition of a pathogen leads to the activation of this immune system, steered by different phytohormones. One of these, salicylic acid, regulates plant responses to biotrophic pathogens that thrive on living host tissue. Typical SA-mediated responses are the production of antimicrobial proteins and metabolites and the strengthening of the cell wall. These responses can occur both locally and systemically. Due to their nature, these responses cost energy and resources that cannot be invested in plant growth and development. This suppression also works the other way around: active growth and developmental processes suppress immunity. This mutual inhibition is called the growth-immunity tradeoff and is actively regulated by the plant. The research in this thesis is focused on the model plant Arabidopsis thaliana (thale cress), in which the SA content is controlled at the level of synthesis and catabolism. Two enzymes that catabolize SA through hydroxylation are the paralogous 2-oxoglutarate Fe(II)-dependent oxygenases DMR6/S5H (DOWNY MILDEW RESISTANT 6/SA 5-HYDROXYLASE) and DLO1/S3H (DMR6-LIKE OXYGENASE 1/SA 3-HYDROXYLASE). dmr6/dlo1 mutants have enhanced SA levels and therefore a constitutively active immune system and enhanced disease resistance. The high SA levels of double mutant plants cause hyperresistance but also dwarfism. On the other hand, overexpression of DMR6 or DLO1 leads to depletion of SA and thus enhanced susceptibility. We use the perturbed SA catabolism of the dmr6/dlo1 mutants and DMR6/DLO1 overexpression lines to investigate the SA-mediated growth-immunity tradeoff. We found that altered expression of DMR6 and/or DLO1 had major effects on the transcriptome that correlated to the plant’s SA content. We found that enhanced SA levels in dmr6/dlo1 mutants caused reduced photosynthetic efficiency and a sped up development and reduced SA levels in DMR6/DLO1 overexpression lines led to reduced pathogen-associated molecular pattern (PAMP)-triggered immune responses. We further identified a significant effect of the genetic background to perturbations in DMR6/DLO1 expression in different Arabidopsis accessions: several Arabidopsis accessions had a reduced growth tradeoff but retained high disease resistance. To systematically investigate the genetics behind regulation of the growth-immunity tradeoff, we further employed a forward genetics screen for restored growth and high resistance in dmr6-3 dlo1 double mutants and identified seven unique zund mutants. These plants carried mutations in known regulators of SA synthesis (ICS1, ISOCHORISMATE SYNTHASE 1), perception (NPR1, NONEXPRESSOR OF PR GENES 1), or signaling (PAD4, PHYTOALEXIN DEFICIENT 4), indicating that a suppression of SA synthesis or SA responses reduces the growth tradeoff in high immunity dmr6-3 dlo1 mutants. Three other zund mutants carried a mutation in the same gene: MED15a (MEDIATOR 15a), a component of the MEDIATOR complex for transcription initiation. We investigate the function of MED15a in the growth-immunity tradeoff in detail, and find that around 80% of dmr6-3 dlo1-induced gene expression changes are genetically dependent on the integrity of two amino acids in the MED15a kinase-inducible (KIX) domain. I discuss the implications of this research for applications to breed for sustainable disease resistance in crops.

Time plays an important role in life. Time is needed to develop from a fertilized oocyte to an adult individual; after adulthood is reached limited time remains for a (healthy) life. This thesis focuses on the complex relationship between organism and time, particularly the relationship between time and gene expression. In chapter 2, a time dependent mechanism which controls gene expression with high precision is discussed. Chapter 3 describes a protocol to measure gene expression levels with spatial resolution in C. elegans. In chapter 4 and 5 this technique is applied to the larval stages and ageing mutants, respectively.

Time plays an important role in life. Time is needed to develop from a fertilized oocyte to an adult individual; after adulthood is reached limited time remains for a (healthy) life. This thesis focuses on the complex relationship between organism and time, particularly the relationship between time and gene expression. In chapter 2, a time dependent mechanism which controls gene expression with high precision is discussed. Chapter 3 describes a protocol to measure gene expression levels with spatial resolution in C. elegans. In chapter 4 and 5 this technique is applied to the larval stages and ageing mutants, respectively.

In this dissertation, we aimed to explore the relationship between the development of networks in the infant's brain and infant behaviour. Ultimately, asking the question: whether differences in characteristics of infant brain networks could explain differences in social competency and behavioural control. This dissertation specifically focused on social competence and self-regulation during infancy, since both types of behaviour develop considerably during the first year of life. Before we could look into this relationship, we needed to make sure that infant EEG networks were reliable. Therefore, in chapter 2, we looked into the reliability of graph theoretical characteristics of infant EEG networks. We found that global metrics, metrics that are averaged over the entire brain, are generally highly reliable in both the theta and the low alpha frequency bands. Local metrics were less reliable. In chapter 3, we looked into the external factors influencing infant EEG data quality. The factors influencing data attrition described in this study can be broadly divided into three groups: child-related factors, testing-related factors, and longitudinal (study-specific) factors. Three child-related factors were found to influence data loss: gender, age, and head shape. Four testing-related factors were found to influence data loss: time of testing, the season of testing, the research assistant present during the experiment, and task length all had considerable influence on data. Lastly, data attrition rates of the first session of testing were found to be related to the second session of testing, underlining possible longitudinal biases in terms of data loss. After confirming acceptable reliability and data quality of our infant EEG data, we looked into the relationship between infant brain networks and behaviour. In chapter 4, we describe the development of the infant connectome during the first year of life and find a reorganization of the theta network between 5 and 10 months old. After this reorganization, the theta network becomes more responsive towards social cues versus non-social cues. Lastly, in chapter 5, we study whether the infant brain network can predict behaviour and vice versa. We find that infant self-regulation at 5 months old predicts brain network optimization at 10 months old. Conversely, we find that total theta brain network strength at 5 months old predicts self-regulation at 10 months old. Underlining the bidirectional relationship between brain networks and behaviour during development. This dissertation shows the promise of studying infant brain networks to explain infant behaviour. Infant brain network characteristics are reasonably reliable and offer us a unique insight into the optimization of the brain in the first year of life.

In this dissertation, we aimed to explore the relationship between the development of networks in the infant's brain and infant behaviour. Ultimately, asking the question: whether differences in characteristics of infant brain networks could explain differences in social competency and behavioural control. This dissertation specifically focused on social competence and self-regulation during infancy, since both types of behaviour develop considerably during the first year of life. Before we could look into this relationship, we needed to make sure that infant EEG networks were reliable. Therefore, in chapter 2, we looked into the reliability of graph theoretical characteristics of infant EEG networks. We found that global metrics, metrics that are averaged over the entire brain, are generally highly reliable in both the theta and the low alpha frequency bands. Local metrics were less reliable. In chapter 3, we looked into the external factors influencing infant EEG data quality. The factors influencing data attrition described in this study can be broadly divided into three groups: child-related factors, testing-related factors, and longitudinal (study-specific) factors. Three child-related factors were found to influence data loss: gender, age, and head shape. Four testing-related factors were found to influence data loss: time of testing, the season of testing, the research assistant present during the experiment, and task length all had considerable influence on data. Lastly, data attrition rates of the first session of testing were found to be related to the second session of testing, underlining possible longitudinal biases in terms of data loss. After confirming acceptable reliability and data quality of our infant EEG data, we looked into the relationship between infant brain networks and behaviour. In chapter 4, we describe the development of the infant connectome during the first year of life and find a reorganization of the theta network between 5 and 10 months old. After this reorganization, the theta network becomes more responsive towards social cues versus non-social cues. Lastly, in chapter 5, we study whether the infant brain network can predict behaviour and vice versa. We find that infant self-regulation at 5 months old predicts brain network optimization at 10 months old. Conversely, we find that total theta brain network strength at 5 months old predicts self-regulation at 10 months old. Underlining the bidirectional relationship between brain networks and behaviour during development. This dissertation shows the promise of studying infant brain networks to explain infant behaviour. Infant brain network characteristics are reasonably reliable and offer us a unique insight into the optimization of the brain in the first year of life.

Introductiecollege voor alle eerstejaarsstudenten Vastgoed & Makelaardij.

Risk-taking behaviour is essential to human life. However, risk-taking behaviour can also compromise healthy development when the costs of risk-taking outweigh its benefits. Think of behavioural problems in childhood, or – later in development - criminal behaviour, delinquency, drug abuse and health-and societal compromising behaviours that have been associated with risk-taking behaviour. Research describing the development of risk-taking behaviour is mainly focused on adolescents and less is known about the development of risk-taking behaviour in elementary schoolchildren. Therefore, we aim to get a better understanding of the development of risk-taking behaviour in childhood. The two overarching research questions in the present thesis are: 1. What is the normative development of risk-taking behaviour in mainstream elementary schoolchildren and (how) are individual differences in risk-taking development associated with externalizing and/or internalizing symptoms? 2. What is the association between adverse social experiences and the development of risk-taking behaviour and subsequent development of maladaptive behaviour? To answer our research questions two different study samples are used. The first sample came from a larger longitudinal project, “Happy Children, Happy Adolescents?”, among Dutch elementary schoolchildren on their behavioural, social-emotional, cognitive and bio-psychological development during the elementary school and the role of interactions with peers and teachers in this development. The second sample came from a longitudinal multigenerational study, “Avon Longitudinal Study of Parents and Children”, on how physical and social environments interact over time with genetic inheritance to affect health, behaviour and development in infancy, childhood, adolescence and then into adulthood. Participants in this project were all from Bristol, UK and surrounding areas. Both datasets include repeated behavioural measures related to risk-taking (risk-taking propensity and sensation-seeking) and information on the social environment of the children (peer victimization, childhood maltreatment and social classroom norms). Jointly, the datasets covered the child and adolescent period from ages 7 – 19 years. Overall, the findings of the present thesis implicate that increases in risk-taking behaviour during the elementary school period is normative in both boys and girls and as such, is nothing to worry about. However, attention should be payed to individual differences and to those who show deviations (both heightened and lowered) in levels and development of risk-taking behaviour during the elementary school period. As, in our studies, heightened risk-taking behaviour is related to the development of externalizing problems and lowered risk-taking behaviour to the development of symptoms of anxiety. Our results imply that even more vigilance on deviating risk-taking behaviour is warranted when children have experiences of victimization. Our results show that experiences of victimization may be related to DNA methylation profiles that have been associated with high sensation-seeking behaviour and in turn with the development of delinquent behaviour in later life. In addition, our results showed that victimized children tend to show norm-defying levels of risk-taking behaviour in their classroom. As such, being victimized may set the stage for a deviating developmental course of risk-taking development that in turn may increase the risk for further development of both internalizing and externalizing problems later in life.

Woensdag 27 oktober jl., vond 's avonds het Renaissance Café plaats in de kerk van Garmerwolde. Het onderwerp was "Tussen droom en data: brede welvaart in het dorp". Dit Renaissance Café maakte onderdeel uit van een landelijke serie om in gesprek te gaan over een nieuwe verhouding tussen stad en platteland, gericht op leefbaarheid. Met name het verbeteren van de leefbaarheid in dorpen door initiatieven vanuit verschillende disciplines, onder andere de kunsten, stond centraal. Het Renaissance Café werd georganiseerd door de Hanzehogeschool Groningen, Kenniscentrum NoorderRuimte, het Kennisnetwerk Krimp Noord-Nederland, Renaissance van het Platteland en Aletta Jacobs School of Public Health.

The synapse is the most characteristic feature of the brain that allows the flow of information encoding our cognitive functions, behavior and memory. Slight perturbations in synaptic function can derive in wide range of psychiatric, neurodevelopmental and neurodegenerative disorders. The aim of this thesis was to investigate the synaptic proteome and interactome in order to gain insights in the molecular mechanisms underlying synaptic function. To this end, we exploited the potential of multiple advanced mass spectrometry methodologies for protein identification, quantification, and protein interaction determination. In chapter 2, I investigated the molecular development of the synapse. This process requires prominent changes of the synaptic proteome and potentially involves thousands of different proteins at every synapse. We analyzed the cortical synaptic membrane proteome of juvenile, adolescent and adult mice brains using iTRAQ-based DDA quantitative proteomics. In several cases, proteins from a single functional molecular entity, e.g., subunits of the NMDA receptor, showed differences in their temporal regulation, which may reflect specific synaptic development features of connectivity, strength and plasticity. We also evaluated the function of Cxadr, a protein with high expression level at early stages and a fast decline in expression during neuronal development. Knockdown of the expression of Cxadr in cultured primary mouse neurons revealed a significant decrease in synapse density. Altogether, these results reveal the expression profile of synaptic proteome during development and provide new insights into the molecular processes underlying synaptogenesis and synapse maturation. In chapter 3, I explored the mechanism behind the synaptic modulation mediated by the metabotropic glutamate receptor 5. mGluR5 plays a major role in the modulation of synaptic function and plasticity, as well as in several brain disorders. Despite robust pre-clinical data, mGluR5 antagonists failed in several clinical trials, highlighting the need for a better understanding of the mechanisms underlying mGluR5 function. Using a proteomic approach, we determined the molecular response of the synapse to a reduction of mGluR5 activity by pharmacological inhibition and gene deletion. In both cases, the most prominent response of the synaptic proteome was the change in protein expression of key mitochondrial pathways. Together with this, we observed morphological and functional alterations of mitochondria in mGluR5 KO synapses. Our findings provide new insight into a functional connection of mGluR5 and specific mitochondrial function. In chapter 4, I applied XL-MS as entry into the synapse interactome, in particular to reveal the architecture and assembly of synaptic protein complexes. As a result, we generated to the first large-scale cross-linking repository in the brain. The reliability of the data was validated by several approaches as we deemed necessary for a recent methodology. In addition, a large part of the crosslink data contains novel information which allowed us to identify novel protein partners, to model protein conformational dynamics, and to delineate within and between protein interactions of main synaptic constituents, such as Camk2, the AMPA-type glutamate receptor, and associated proteins. Given the molecular complexity of the synapse and the large amount and depth of the data generated, we provided the complete dataset as an interactive web-based platform for further investigations (http://xlink.cncr.nl). Together, we generated one of the largest cross-linking collections that provided new entries into exploration of protein structures and interactions. Collectively, the application and development of multiple proteomic methodologies allowed us to reveal several aspects of the molecular architecture of the synapse, including protein composition, function, structure and interaction. Beyond the new insights uncovered for specific proteins in this thesis, the data resources generated can be further used for probing additional proteins and contributes to improve our understanding of synapse function and brain disease.