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
This thesis aims to investigate the effect of tripartite interaction between microbial inoculants, the plant, and herbivore insects on the rhizosphere microbiome and volatilome. We investigated the... Show moreThis thesis aims to investigate the effect of tripartite interaction between microbial inoculants, the plant, and herbivore insects on the rhizosphere microbiome and volatilome. We investigated the rhizosphere microbiome and volatilome of tomato plants exposed to insect herbivory and/or inoculated with beneficial microbes known to trigger ISR. First, we reviewed the abiotic and biotic factors that impact the success of ISR microbial inoculants (Chapter 2). Then, we tested microbial inoculants against different stresses and experimental conditions to compare interactions in variable contexts (Chapter 3). Next, we explored the impact of insect herbivory aboveground, on the volatile and microbial belowground compartment. In Chapter 4 we explored root volatiles under stress in two tomato species to evaluate the genotype impact on the stress-induced root volatilome. In Chapter 5, we studied the impact of endosymbiotic fungi arbuscular mycorrhizal fungi (AMF) on root volatiles in an in vitro bioassay and in a greenhouse setup with herbivory-stressed plants. In Chapter 6, we compared the effect of four phylogenetically diverse bacteria and fungi, inoculated as single-species and as a synthetic community, on the rhizosphere microbiome assembly and volatilome in herbivory-stressed plants. Overall, this thesis delves into overlooked interactions providing novel data on belowground plant-microbe interactions. Show less
Polymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug... Show morePolymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug resistant Gram-negative bacteria.In this thesis, we describe the development and synthesis of analogues of polymyxin, aimed at reducing its associated nephrotoxicity. Analogues were made by semisynthesis, with modifications introduced mostly in the exocyclic portion of the molecule. Especially the introduction of a disulfide bond within the linked lipid helped in reducing the toxicity of the molecules, as evidenced by testing on proximal tubule epithelial cells. For most potent analogues, the antimicrobial activity was completely retained.In addition, this thesis describes studies on the mechanism of action of polymyxin, mostly based on the full stereoisomer of polymyxin B4. This analogue lacks antimicrobial activity, indicating its original stereochemistry to be of utmost importance for its use as an antibiotic.Hybrids based on polymyxin B derivatives are described, addressing non-conventional targets. A hybrid with vancomycin (typically active on Gram-positive bacteria only) shows activity on Gram-negative bacteria. A polymyxin-based hybrid coupled to a peptide with a beta-hairpin motif addresses Gram-negative bacteria, presumably by binding to outer membrane protein BamA. Show less
Bierman, T.V.; Vrieling, K.; Zwieten, R. van; Kodger, T.E.; Marcel, M.; Bezemer, T.M. 2024
Arthropod pests cause significant problems in agricultural crops all around the world. As chemical pesticide use becomes less desired, there is a need for alternative methods of pest control.... Show moreArthropod pests cause significant problems in agricultural crops all around the world. As chemical pesticide use becomes less desired, there is a need for alternative methods of pest control. Inspired by the natural adhesiveness of arthropod trapping plants, we examined the effectiveness of adhesive droplets made from oxidised and cross-linked plant-derived oils for control of western flower thrips. Two filter paper droplet adhesiveness assays and three detached chrysanthemum leaf assays were carried out to test efficacy against thrips. Suspensions containing adhesive droplets and other constituents were applied to filter papers and leaves via spraying or dipping. On filter papers, droplets made from oxidised rice germ oil (RGO) of different sizes caught 40–93% of thrips. Droplets made of a mixture of sunflower, olive, and linseed oil (MIX) caught up to 94% of thrips. Likewise, adhesive droplet-treated filter papers showed higher thrips mortality than untreated or control solution-treated filter papers. On chrysanthemum leaves, thrips were caught by both RGO (up to 40%) and MIX droplets (up to 20%) and thrips damage and reproduction were reduced. On MIX-treated leaves, thrips mortality was also increased. Within treatments, droplets of different size classes occurred and larger droplets were more effective at catching thrips in general. Droplets were also robust to rinsing with water, which is of importance for their application in horticulture. In conclusion, adhesive droplets made from edible plant oils show potential for use in control of western flower thrips. Show less
Members of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and... Show moreMembers of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and applications. However, despite its prevalence in nature, the characterization and classification of Bacillus remain challenging due to its complex and ever-evolving taxonomic framework. This review addresses the current state of the Bacillus taxo- nomic landscape and summarizes the critical points in the development of Bacillus phylogeny. With a clear view of Bacillus phylogeny as a foundation, we subsequently review the methodologies applied in identifying and quantifying Bacillus, while also discussing their respective advantages and disadvantages. Show less
Alvarez van Tussenbroek, I.; Knörnschild, M.; Nagy, M.; Cate, C.J. ten; Vernes, S.C. 2024
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
Oratie uitgesproken door Prof.dr. A.F.J. Ram bij de aanvaarding van het ambt van hoogleraar Schimmelgenetica en Biotechnologie aan de Universiteit Leiden op vrijdag 9 februari 2024
The haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is... Show moreThe haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is well supported by the results of several molecular phylogenetic studies, which shed light on their relationships and circumscriptions, and thus also contributed to identify many remaining problems. Dicranidae ordinal classification is not congruent with current relationship hypotheses and is not supported by morphology. Morphological circumscriptions of some families do not correspond to monophyletic groups. Furthermore, the monophyly of many families and genera with weak morphological circumscriptions remains to be tested. In this thesis, systematics and relationships of the leucobryoid mosses and some families and genera segregated from the former Dicranaceae s.l. were studied using molecular phylogenetic methods. 37 out of the 38 haplolepideous moss families were represented by markers from the three genomes (nrITS, nad5, trnS-trnF, atpB-rbcL). Phylogenetic reconstructions were based on maximum parsimony, maximum likelihood, and Bayesian inference. Ancestral state reconstructions, phylogenetic network analysis (NeighborNet), and relationship hypothesis testing (Shimodaira-Hasegawa test) were performed to contribute to the interpretation of the results of the phylogenetic reconstructions. Morphological circumscriptions were evaluated and improved whenever possible, in line with the results of all analyses performed. Show less
Phenological responses to climate change frequently vary among trophic levels, which can result in increasing asynchrony between the peak energy requirements of consumers and the availability of... Show morePhenological responses to climate change frequently vary among trophic levels, which can result in increasing asynchrony between the peak energy requirements of consumers and the availability of resources. Migratory birds use multiple habitats with seasonal food resources along migration flyways. Spatially heterogeneous climate change could cause the phenology of food availability along the migration flyway to become desynchronized. Such heterogeneous shifts in food phenology could pose a challenge to migratory birds by reducing their opportunity for food availability along the migration path and consequently influencing their survival and reproduction. We develop a novel graph-based approach to quantify this problem and deploy it to evaluate the condition of the heterogeneous shifts in vegetation phenology for 16 migratory herbivorous waterfowl species in Asia. We show that climate change-induced heterogeneous shifts in vegetation phenology could cause a 12% loss of migration network integrity on average across all study species. Species that winter at relatively lower latitudes are subjected to a higher loss of integrity in their migration network. These findings highlight the susceptibility of migratory species to climate change. Our proposed methodological framework could be applied to migratory species in general to yield an accurate assessment of the exposure under climate change and help to identify actions for biodiversity conservation in the face of climate-related risks. Show less
Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for... Show moreSiderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly inf luenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of f luorescent Pseudomonas spp. and found that the Bacillus–Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria. 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
Jia, Y.; Wang, M.; Lambers, P.H.; Andel, T.R. van 2024
