In this thesis, I focused on studying the above- and belowground interactions of J. vulgaris from a plant-soil feedback (hereafter, PSF) perspective. I investigated the temporal variation of... Show moreIn this thesis, I focused on studying the above- and belowground interactions of J. vulgaris from a plant-soil feedback (hereafter, PSF) perspective. I investigated the temporal variation of negative PSF and examined the effects of root-associated bacteria on plant performance and aboveground herbivores. Additionally, I tested the role of PSF in relation to plant population structure and the significance of soil legacy effects in natural conditions. The findings reveal that temporal dynamics in PSF are driven by changes in plant sensitivity and in the soil microbiome. Although bacteria isolated from J. vulgaris roots can negatively affect plant performance, they can also affect aboveground herbivores and other plant species. Consequently, these bacteria may not be suitable for biological control of J. vulgaris. Moreover, I discovered that soil nematodes can mediate plant-plant interactions, but often favoring J. vulgaris. In my field work, I detected soil legacy effects, but seedling recruitment spatial patterns of J. vulgaris were not soil-mediated. The insights gained from studying PSF and above- and belowground interactions have the potential to reshape traditional approaches employed in controlling invasive plants. This thesis emphasizes the importance of transitioning PSF experiments from indoor to outdoor settings considering various influencing factors simultaneously. Show less
Human vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross... Show moreHuman vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross-species research sheds light on the origins of musicality by investigating whether these traits are shared by nonhuman species. Songbirds, notably zebra finches, serve as valuable models due to their complex vocalizations and similarities to humans in auditory perception. My thesis explored zebra finches' sensitivity to spectral and temporal sound features. Chapter 2 examines the influence of song duration and spectral characteristics on song discrimination, while Chapter 3 tests song preferences. Chapter 4 investigates sequential and spectral feature recognition. Chapter 5 focuses on melody recognition. Zebra finches demonstrate perceptual flexibility, adapting focus based on stimulus characteristics. These findings underscore the importance of training conditions and stimulus nature in shaping auditory perception. Overall, my thesis enhances understanding of auditory cognition and cognitive flexibility among songbirds. Show less
Comparative neurobiology allows us to investigate relationships between phylogeny and the brain and understand the evolution of traits. Bats constitute an attractive group of mammalian species for... Show moreComparative neurobiology allows us to investigate relationships between phylogeny and the brain and understand the evolution of traits. Bats constitute an attractive group of mammalian species for comparative studies, given their large diversity in behavioural phenotypes, brain morphology, and array of specialised traits. Currently, the order Chiroptera contains over 1,450 species within 21 families and spans ca. 65 million years of evolution. To date, 194 Neotropical bat species (ca. 13% of the total number of species around the world) have been recorded in Central America. This study includes qualitative and quantitative macromorphological descriptions of the brains of 12 species from six families of Neotropical bats. These analyses, which include histological neuronal staining of two species from different families (Phyllostomus hastatus and Saccopteryx bilineata), show substantial diversity in brain macromorphology including brain shape and size, exposure of mesencephalic regions, and cortical and cerebellar fissure depth. Brain macromorphology can in part be explained by phylogeny as species within the same family are more similar to each other. However, macromorphology cannot be explained by evolutionary time alone as brain differences between some phyllostomid bats are larger than between species from the family Emballonuridae despite being of comparable diverging distances in the phylogenetic tree. This suggests that faster evolutionary changes in brain morphology occurred in phyllostomids — although a larger number of species needs to be studied to confirm this. Our results show the rich diversity in brain morphology that bats provide for comparative and evolutionary studies. Show less
The plant hormone auxin regulates plant growth and development through polar cell-to-cell transport-generated maxima and minima. PIN FORMED (PIN) auxin efflux carriers determine the direction of... Show moreThe plant hormone auxin regulates plant growth and development through polar cell-to-cell transport-generated maxima and minima. PIN FORMED (PIN) auxin efflux carriers determine the direction of this auxin flow through their asymmetric placement on the plasma membrane (PM). In Arabidopsis thaliana (Arabidopsis), the PM-associated protein kinase PINOID (PID) regulates PIN localisation and thereby auxin transport polarity by phosphorylating these carriers in their central cytoplasmic loop. PID in turn interacts with the calmodulin-like protein TOUCH3 (TCH3) in response to elevated cytosolic calcium, which dissociates PID from the PM and inhibits its kinase activity. In this thesis, we show that PID also interacts with 10 other CALMODULIN/CALMODULIN-LIKE proteins, which together with TCH3 form a confined clade in the CaM/CML family. The CaM/CML binding domain in PID was found to map to an amphipathic alpha-helix inserted in the catalytic kinase core. Disruption of this alpha-helix did not affect PID kinase activity, but impaired both its PM association and the interaction with the CaM/CMLs, making the kinase “untouchable”. Expression of “untouchable” PID versions in the pid mutant background revealed that proper calcium-CaM/CML-PID signalling is essential to maintain the robust spiral phyllotaxis that is typical for the Arabidopsis inflorescence. Show less
Given the accelerating appearance of antimicrobial resistance, there is an urgent need for more fundamental research into novel antibiotic strategies. The work in this thesis helps to address this... Show moreGiven the accelerating appearance of antimicrobial resistance, there is an urgent need for more fundamental research into novel antibiotic strategies. The work in this thesis helps to address this global problem by developing new antibiotic compounds, inspired by the antibacterial mechanisms of the natural antibiotic bacitracin. By unravelling the unique mechanism of action that bacitracin employs, we discovered that the inclusion of a small hydrophobic group in key locations of the molecule results in a dramatic enhancement of antibacterial activity, in some cases more than 100 times more potent than bacitracin. Crucially we found that the most potent analogues are particularly active against antibiotic-resistant bacteria including those bearing clinically challenging resistance genes. In doing so we have developed potent next-generation variants of this classic antibiotic and have taken important steps in the fight against antimicrobial resistance. Show less
Grafieken zijn heel geschikt om veel en complexe informatie weer te geven: ze bieden in één oogopslag overzicht en duidelijkheid. Bovendien hebben ze een objectieve uitstraling waardoor ze het vaak... Show moreGrafieken zijn heel geschikt om veel en complexe informatie weer te geven: ze bieden in één oogopslag overzicht en duidelijkheid. Bovendien hebben ze een objectieve uitstraling waardoor ze het vaak goed doen als argument bij een bewering: “de cijfers liegen niet.” Behalve als ze dat wel doen, en dat komt helaas maar al te vaak voor. Daarom hier een lesje in het doorprikken van nepnieuws met misleidende grafieken. Show less
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial... Show moreDevelopments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation. Show less
Hoe snel groeit een kind? Welke leeftijdsgroep krijgt het vaakst de griep? En welk land heeft gemiddeld de langste mannen? Vaak wordt het antwoord op dit soort vragen gepresenteerd in een grafiek.... Show moreHoe snel groeit een kind? Welke leeftijdsgroep krijgt het vaakst de griep? En welk land heeft gemiddeld de langste mannen? Vaak wordt het antwoord op dit soort vragen gepresenteerd in een grafiek. Een grafiek geeft je in één oogopslag een beeld van hoe iets in elkaar steekt. Toch? ,,Niet altijd”, vertelt Winnifred Wijnker. ,,Dat de ene staaf veel hoger is dan de andere, betekent niet altijd dat de verschillen ook heel groot zijn.” Show less
The mycorrhizal symbiosis is among the most widespread species interactions on Earth. This thesis focuses on orchid mycorrhiza, a unique mycorrhizal type that has caught scientists’ attention for... Show moreThe mycorrhizal symbiosis is among the most widespread species interactions on Earth. This thesis focuses on orchid mycorrhiza, a unique mycorrhizal type that has caught scientists’ attention for centuries. By merging the concepts and approaches of molecular phylogenetics, microbial community ecology, and plant ecophysiology, this thesis provides an overview of the evolution and ecology of orchid mycorrhizal interactions from both the fungal and plant perspective, and from the global to the local scale. In this thesis, the variation in fungal associations in space and in time is a central topic, which was inferred by analyses on phylogenetic signals and variation in fungal community structure and also captured by empirical experiments using metabarcoding approaches and quantitative ddPCR. Based on the insights gained in this thesis and that of previous studies, this thesis proposes several directions for future studies to deepen our understanding of the evolution, ecophysiology, and molecular biology of mycorrhizal symbiosis, and thus to benefit orchid conservation and ecosystem restoration. Show less
Songbirds as vocal learners learn their songs and song preference from social tutors. Tutor choice for both song and preference learning are important to characterize for understanding individual... Show moreSongbirds as vocal learners learn their songs and song preference from social tutors. Tutor choice for both song and preference learning are important to characterize for understanding individual learning performance and cultural transmission of song. It is unclear whether early learned song preferences are generalised to songs similar to the tutor song and how simple versus complex early social environment might affect tutor choice and learning contents. This thesis addresses these questions in the zebra finch, the primary avian model for vocal learning studies, by reviewing the existing literature on song and preference learning and conducting three experiments. In these experiments, family raised female zebra finches were tested with a stimulus set of four songs along a gradient of decreasing similarity with the song they learned early in life. A breeding and song learning experiment comparing zebra finches raised with a single versus multiple tutors was conducted. The results suggest that female zebra finches generalise their early learned preferences for a specific song to other unfamiliar songs along a gradient of similarity. Social environment and individual differences can affect tutor choice for both song and preference learning in this colonial species. Show less
This thesis describes how different colours of light affect various aspects of the growth and development of Arabidopsis and tomato plants. In the first chapter, we review the current knowledge of... Show moreThis thesis describes how different colours of light affect various aspects of the growth and development of Arabidopsis and tomato plants. In the first chapter, we review the current knowledge of light receptors and different light-regulated processes. In the second chapter we investigated the effect of direct illumination of roots. In the third chapter we presented an overview of the phenotypes that arise when plants are grown in white, red or blue light. In the fourth and fifth chapter we further investigate the stem and flowering phenotypes that were observed in the different light conditions. Altogether we show that red and blue light often act antagonistically, and that some light-regulated processes may be species- or age-specific. Show less
Zdouc, M.; Bayona Maldonado, L.M.; Augustijn, H.; Soldatou, S.; Jonge, N. de; Jaspars, M.; ... ; Hooft, J.J.J. van der 2023
Striga hermonthica, commonly known as witchweed, infests major cereal crops in Sub-Saharan Africa causing severe yield losses and threatening the livelihood of millions of resource poor farmers.... Show moreStriga hermonthica, commonly known as witchweed, infests major cereal crops in Sub-Saharan Africa causing severe yield losses and threatening the livelihood of millions of resource poor farmers. Despite the use of herbicides, Striga-resistant crop varieties and agronomic practices to mitigate the impact of Striga, these are not effective on their own and require high monetary investments by smallholder farmers. My PhD research focuses on the potential of soil microbes to disrupt the early stages of the parasite’s life cycle through the production of volatile organic compounds. More specifically, we developed a computer vision tool that enabled the large-scale screening of a large bacterial collection for its functional potential to suppress Striga seed germination by naturally produced volatile compounds. This was complemented with the identification of several Striga-suppressive volatile compounds and studies into their genomic regulation. We developed a new approach of ‘precursor-directed activation’ of Striga-suppressive soil microbes by amending field soils with amino acid precursors to suppressive volatile compounds. This strategy will enable better deployment of volatile-mediated Striga suppression under field settings, by steering its production in situ and by aiding in the development of future control methods with higher efficacies and lower application costs Show less
Een staafdiagram van de PvdA geeft een geflatteerd beeld van de verhoging van het minimumloon die PvdA en GroenLinks bepleiten. De cijfers kloppen, maar de grafiek stelt het verschil met het... Show moreEen staafdiagram van de PvdA geeft een geflatteerd beeld van de verhoging van het minimumloon die PvdA en GroenLinks bepleiten. De cijfers kloppen, maar de grafiek stelt het verschil met het huidige minimumloon groter voor dan het is. ‘Wij hebben bewust voor deze weergave gekozen’, reageert de PvdA-woordvoerder. Show less
Een lijngrafiek van de NOS geeft een overdreven beeld weer van de toename in het aantal doden na politiegeweld in de VS. De toename is er, maar niet zo extreem als de grafiek suggereert.
Calamus javensis is polymorphic. Morphometry and molecular approach resulted in all names used in the complex are regarded as synonyms of C. javensis except C. tenompokensis, which is retained as a... Show moreCalamus javensis is polymorphic. Morphometry and molecular approach resulted in all names used in the complex are regarded as synonyms of C. javensis except C. tenompokensis, which is retained as a distinct species. One variety is here recognized, C. javensis var. polyphyllus (including C. acuminatus) Show less
In een misleidende infographic over de gemiddelde lengte van volwassen mannen zijn Nederlanders reuzen en Indonesiërs dwergen. We laten in een paar stappen zien wat er fout ging en hoe je dat kunt... Show moreIn een misleidende infographic over de gemiddelde lengte van volwassen mannen zijn Nederlanders reuzen en Indonesiërs dwergen. We laten in een paar stappen zien wat er fout ging en hoe je dat kunt corrigeren. Show less
Sound is everywhere in the marine environment and hearing is therefore a very important for stimuli for fish. They use sound for orientation and communication, during migration, aggregation and... Show moreSound is everywhere in the marine environment and hearing is therefore a very important for stimuli for fish. They use sound for orientation and communication, during migration, aggregation and spawning, but also for detection of prey and predators. Understanding how fish are effected by sound has become increasingly important in light of the increasing contribution of noise produced by human activity at sea. In this thesis, I investigated the effects of two anthropogenic sound sources in relation to the movement behaviour of free-swimming Atlantic cod (Gadus morhua) in the North Sea: seismic surveying for the exploration of the seabed and pile driving during the construction of offshore windfarms. Results from the two sound exposure studies demonstrated that both seismic and piling sound effect the behaviour of cod. Exposure to a seismic survey resulted in reduced activity during exposure and fish leaving the area earlier in the year. Piling did not result in leaving but did cause cod to move closer to the hard bottom structures. Ultimately, these insights will bring us one step closer towards recognising the effects of anthropogenic noise on the behaviour of individual marine fish and the potential consequences this may have at population level. Show less
