We perform multidisciplinary research at molecular, cellular, and organismal levels of animal biology to increase fundamental understanding of health and disease.

The Animal Sciences cluster fosters collaboration between researchers with expertise in molecular cell biology, immunology, physiology, behavioural biology, and evo-devo research. As detailed under the links on this page, Animal Sciences participates in all of the institute wide-research themes: Bioactive Molecules, Development & Disease, Biodiversity & Evolution, and Host-Microbe Interactions. In brief, Animal Sciences contributes in the following ways:

Bioactive Molecules:  Animal Sciences’ contribution to the Bioactive Molecules research theme includes research on molecules from natural sources, such as plants, insects, and snake venom, with the aim to identify novel anti-cancer, anti-inflammatory, anti-microbial, and anti-diabetic agents.

To this end, mammalian cell-based screens are used in combination with zebrafish models for cancer, inflammation, infectious disease, and anxiety. These disease models are also employed for drug repurposing screens using libraries of FDA-approved drugs. Utilizing omics technologies (transcriptomics, metabolomics and proteomics) or fluorescence-based imaging (cell-based screens and transgenic zebrafish reporter lines) the effects of drugs can be determined at whole organism level, providing insight into metabolic and hormonal responses, and the signalling processes underlying their mechanism of action.

We also explore the possibilities of zebrafish models for testing drug delivery systems, for evaluating photoactivatable drugs, and for pharmacokinetics and pharmacodynamics studies in drug development. We aim to get more mechanistic insight into the efficacy of drugs in various diseases and translate this knowledge to clinical applications.

Development & Disease: Animal Sciences’ contributions to the Development & Disease research theme include the mechanisms and evolution of embryonic development, the development of cognitive mechanisms, and animal models for understanding mechanisms of human disease.

We study the embryonic development of invertebrates, such as egg development of beetles, as well as vertebrates, such as limb development of birds and reptiles and vascular development in cell culture and zebrafish. For these studies, we develop cell culture and mathematical models alongside animal models. In our studies of cognitive development, we focus on learning and processing of vocal and visual signals in birds,  and the interrelations between acoustic stimuli, behaviour and physiological health in birds and fish. Our zebrafish models for human disease focus on immune-related diseases, including infectious diseases such as tuberculosis, salmonellosis, and aspergillosis, on metabolic diseases such as diabetes, and on cancer using human cancer cell xenografts.

Biodiversity & Evolution: Animal Sciences’ contributions to the Biodiversity & Evolution research theme include evo-devo research, the evolution of cognitive and behavioural traits, and the evolutionary mechanisms of stress adaptation. This research involves both indoor and outdoor studies.

An example of evo-devo research is the comparative embryology of birds and reptiles to understand the evolution of limb development. Another example is the study of evolutionary novelties, such as the insect egg membrane that enabled the transition from water to land. A computational approach is taken to model the origins of multicellular life. Genomic data are used to study gene flow between closely related species in hybrid zones and genomic re-arrangements in balanced lethal systems.

The research on cognitive and behavioural traits addresses similarities between human speech and bird song, including grammatical and musical abilities. Birds are also used to study the evolution and phenotypic plasticity of sexually selected sensory traits and the evolution of acoustic signals. Research into stress adaption focuses on the impact that noise related to human activities has on birds and underwater animals (fish, sea mammals). Finally, the zebrafish is used as a model to study to stress coping styles and the relationship with the biological clock.

Host-Microbe Interactions: Animal Sciences’ contributions to the Host-Microbe Interactions research theme focus on the interaction of animal hosts with pathogenic microbes but also the beneficial role of the gut microbiome.

Mammalian macrophages and zebrafish larvae are used to study the intracellular stages of bacterial pathogens (Mycobacterium, Salmonella, Staphylococcus) and pathogenic fungi (Aspergillus) and the interactions of pathogens with host processes such as inflammatory signalling and autophagy. In collaboration with Microbial Sciences, we also study the interaction of cholera bacteria with the zebrafish gut epithelium. Zebrafish reared germ-free or colonized by defined bacterial populations are used to study how the microbiome shapes immune responses.

In addition, the microbiota and host-microbiome interactions are studied by computational modelling. Research in insects has identified the outer membrane (serosa) of beetle eggs as an immune organ and the signalling pathways involved are currently under study.

Studying the origins of our capacity for music

We are looking for enthusiastic parrot owners who want to contribute to our understanding of musicality: the capacity to perceive, make, and appreciate music. Is musicality a uniquely human capacity? Or is it something we share with many other animals, and hence a capacity that has a long evolutionary history?

This citizen science project is part of a larger research effort to characterise the potential biological basis of musicality. A core component of musicality is relative pitch, a skill that allows us to recognise a certain song or melody, even when it is played a few tones higher or lower, or faster or slower (see box). We humans attend to the relations between the tones, and not to the individual frequencies of each tone. It has long been thought that this ability is what makes humans specifically musical. Interestingly, most birds are particularly good at distinguishing different melodies by their absolute frequencies. They seem to have absolute pitch (which is a rare talent in humans).

Discovering the musical skills of parrots

In this particular project, we are interested to see if this difference in music perception and cognition is one of degree or one of kind. It might well be that birds are more flexible than thought before. Especially if they are singing in their natural or familiar habitat. We aim to investigate how well parrots recognise and imitate melodies, and, especially, how flexible they are. We invite bird owners to participate in our World-Wide Bird Singalong Project to discover the musical skills of parrots and other songbirds. We need parrot owners to help us with the following:

We would first like to receive a video of your parrot singing a song. You can upload this video in the registration form when applying to participate in our study. We would also like to know how your parrot was taught this song. Did it learn it from a video on social media? Or did you teach it yourself by singing or whistling to your parrot? You can fill in this information on the registration form.

Altered version of the song
We will then analyse the singing of your parrot and create a slightly altered version of the song. This altered version of the song will either be a few notes higher or a few notes lower than the original song your parrot learned. We will contact you and send this altered song back via e-mail.

Playback and recording
Finally, we would like to ask you to playback the altered songs multiple times to your parrot and subsequently record your parrot singing the song again. We would like to receive this video to analyse the singing of your parrot again. We suspect that your parrot will match the pitch changes we made to the song by also singing at a higher or lower pitch than usual. This would potentially mean that your parrot is able to use relative pitch! Something that is rarely found in animals and believed to be unique for humans!

Relative versus absolute pitch

Relative and absolute pitch are two skills that can both be used to perceive and memorise pitch in music. Most animals, as far as we know, use a form of absolute pitch in recognising melodies, most humans use relative pitch. 

Absolute pitch: to recognise a note by its pitch, which is determined by the fundamental frequency of the sound wave.
Absolute pitch, also known as ‘perfect pitch’ refers to being able to recognise a sound by its pitch and label it (is it a C or a D?) without a reference. For someone with ‘perfect pitch’ this goes as effortlessly as most humans label colours. The first part of the skill, memory for pitch, is widespread in humans and animals. Categorising or labelling a pitch, however, is rare in humans (estimated as only 1 in 10,000 people).

Relative pitch: to recognise a song by the interval structure or contour of the melody (is a note higher or lower than the note before?)
Relative pitch means recognising the same tune even if it’s played a few tones higher or lower. We use relative pitch to listen to the relative difference between musical notes. This way, humans can easily recognise a melody that is played a few tones higher or lower than the original. Birds appear to have great difficulty in classifying pitch-shifted sounds.

Follow the Bird Singalong Project on Instagram!

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Read more about Bird Sing Along Project:

Nick Dam over schermverslaafde en zingende papegaaien

Wanted: Singing parrots - is our musicality unique?

Music sensitivity parrots put to the test

Michelle Spierings aims for Klokhuis Wetenschapsprijs met musicality animals

The mission of the Plant Sciences cluster is to contribute to the sustainable production of high-quality crops, flowers and high-value bio-based products, and to contribute to the maintenance and restoration of biodiversity in natural ecosystems. This is realised by generating fundamental knowledge of basic biological processes related to the development of plants and by unravelling their interactions with the environment.

The Plant Sciences cluster of the IBL hosts scientists from diverse fields of expertise. On the one hand, molecular geneticists explore plant-microbe interactions to develop tools for the directed modification of the plant genome. On the other hand, plant ecologists investigate how microbiomes affect plant health, growth and community composition with a specific focus on the role of secondary metabolites in plant-microbe and plant-insect interactions. In addition, a combination of genetics, molecular cell biology and biochemistry is used to understand plant developmental processes with a focus on developmental switches and how plants adapt to environmental signals and stresses.

Plant Sciences contributes to the four IBL research themes in the following ways:

Bioactive molecules: Plant Sciences' contribution to the Bioactive Molecules research theme is to identify new plant bioactive molecules, and unravel their mechanisms of action in plant development or health, and the regulatory networks and (bio)synthetic pathways required for their production.

As photosynthetic, autotrophic organisms producing an enormous variety of natural ingredients, plants are one of the richest sources for bioactive molecules. Plant-originated bioactive molecules are being used in different fields of life sciences, such as pharmaceutical (e.g. anticancer, anti-inflammatory or antimicrobial compounds) and agricultural sciences (e.g. hormone-like compounds that trigger specific developmental- or defense responses in plants).

The first aim of our phytochemistry research lies in discovering leads for bioactive compounds. This is not only based on conventional approaches, focussing on the chemistry itself, but also on investigating the plant systems where the compounds are derived from. In particular, a fundamental question in plant physiology is how plants realize the biosynthesis of a wide-range of metabolites, even though many of them are not soluble in water? This has led to the discovery of a new group of Deep Eutectic Solvents based on common plant compounds, so-called natural deep eutectic solvents (NADES), that are currently being applied as green extraction solvents for cosmetics, drug delivery systems for pharmaceuticals or as food additives.

In collaboration with other IBL clusters and institutes, the identified and produced bioactive molecules of plants are further developed into pharmaceuticals (e.g. lead compounds or drug delivery systems), agricultural products (e.g. hormones, herbicides, pesticides, or insecticides), functional foods or cosmetics (e.g. extraction and emulsifying reagents).

In addition to the identification of the molecules in plants, an important part of the research in the Plant Science cluster aims at unravelling their mechanisms of action, and the regulatory networks and (bio)synthetic pathways required for their production.

Development & Disease: Plant Sciences' contribution to the Development & Disease research theme is to unravel the processes that allow plants to adapt to changing abiotic and biotic environmental conditions or stresses, with the aim to contribute to the sustainable production of food, flowers and bio-based products using crop plants that are more resilient to adverse growth conditions caused by the global climate change.

Members of the plant kingdom are mostly sessile organisms that cannot move around when environmental conditions become adverse for their survival. As such, they have developed a variety of mechanisms to cope with stress conditions such as shade, cold, heat, drought, herbivory or pathogen attacks. An important defense mechanism is provided by the amazing capacity of plants to adapt their growth and development to changes in environmental conditions. The key to this adaptive development lies in the presence of stem cell groups or meristems that allow plants to continuously form new tissues or organs during their life time, which is important for recovery from herbivory or drought- or heat stress, but also allows the plant to explore their environment and optimally position these organs to sources of nutrients, water and light. Apart from these developmental mechanisms, plants have also developed a plethora of strategies to defend themselves against herbivory and pathogen attacks, such as hairs on leaves (trichomes) and/or secondary metabolites to fend of herbivory by insects or signalling mechanisms that provide systemic resistance to bacterial or fungal attacks.

Within the Development & Disease theme, the research focusses on the role of plant hormones and transcription factors in adaptive growth and development on the one hand and in defence against insect and pathogen attacks on the other hand. The plant hormone auxin, or indole-3-acetic acid (IAA), is a central regulator of plant development, and we study how it directs adaptive growth and development. In addition, the role of auxin, other hormones and transcription factors is studied in plant developmental phase transitions, -longevity and -stress resilience. Resistance of plants to pest and pathogens is to a large extend determined by their metabolomic profile and the way this profile is changed after being attacked. Our fundamental research on signaling and regulation of metabolic pathways concentrates on jasmonic acid (JA) signaling, an important signaling pathway in relation to herbivore attack, and salicylic acid (SA) signaling, an important signaling pathway in relation to pathogens.

In view of the plethora of available genome sequences and large genome wide expression data sets and increasingly detailed and complex signalling pathways in development and disease, bio-informatics and mathematical modelling have become of crucial importance in this research theme.

Biodiversity & Evolution: Plant Sciences' contribution to the Biodiversity & Evolution research theme is to understand what are the key drivers of plant biodiversity during evolution with a focus on plant life history and resilience traits and develop tools to restore and maintain plant biodiversity.

Plants during evolution have adopted to changing environmental conditions by modifying their life history strategy. Annual, monocarpic (flowering once) plants typically avoid adverse conditions by growing when conditions are favourable, and by flowering and producing off spring as soon as unfavourable conditions arise. In contrast, perennial, polycarpic (flowering multiple times) plants develop hardy structures, such as root stocks, bulbs or wood, that allow them to survive adverse conditions, and to continue growth in the next growing season. A recently identified class of nuclear proteins involved in the switch from juvenile to adult life phase has related transcription factors in humans, connecting this research to aging in humans. Currently, the role of these nuclear proteins as key switches between monocarpic (flowering once) and polycarpic (flowering multiple times) life history strategies in plants is investigated. In addition, these proteins seem to promote wood formation in plants, and together with Naturalis their role in the evolution of secondary woodiness in plants is investigated.

Plants produce an overwhelming array of secondary metabolites that play a primary role in the relation of a plant and its environment. Understanding the evolution and maintenance of this diversity is a fundamental research line within the Plant Sciences cluster. This research line has a strong focus on secondary metabolites, how their composition is changed by the soil microbiome, and how this affects plant-insect interactions. Of special interest are the interacting effects of metabolites. Evolutionary changes in the plant’s defense system are studied a.o. in invasive plant species. This research finds its application in contributing to the development of more resistant and more healthy foods (e.g. tomatoes, carrots, strawberries) and more resistant flowers (e.g. chrysanthemum).

Host-Microbe Interactions: Plant Sciences' contribution to the Host-Microbe Interactions research theme is to dissect how microorganisms and microbiomes interact with the plant host and the insects on those plants, and how these insights may be harnessed to improve plant growth and health, by steering microbiome composition and in part by plant genome editing.

The success of plants is strongly determined by their interaction with the soil microbial community. Likewise the composition of the soil microbial community is strongly determined by the plants growing in a soil. Plants leave a legacy in the soil through this effect. In this research line we examine how plants influence the microbiome in the soil in which they grow, and how these changes influence other plants that grow later in the soil, and the insects on those plants. We examine the connection and role of microbiomes in soils, plants and aboveground insects, and study how to manipulate the soil microbial community to increase plant resistance to above ground herbivores, to increase plant production. In natural ecosystems such as grasslands and heathlands, we study how we can steer the composition of soil communities with soil inoculation to enhance the biodiversity and functioning of these ecosystems and to restore degraded ecosystems.

For many generations the Netherlands has a world leading position in classic plant breeding. The obvious disadvantage of classic breeding is that it takes a very long time to get the results that are wanted. To keep the leading position in plant breeding and to be able to create the plants that meet the demands of the future, novel strategies for plant genome modification are needed. Within the Plant Sciences cluster fundamental knowledge on plant genome editing is generated by (i) the “Agrobacterium” research that studies plant-microbe interaction, and (ii) the DNA repair research both with important applications in biotechnology, and the latter also with important applications in relation to health related topics.

In Microbial Sciences, we perform multidisciplinary research to understand the structure and function of microbes at all levels of biological organization, from small molecules and cellular structures at atomic resolution to multicellular communities.

We investigate how microbes sense and respond to their environment and interact with other organisms, and harness Nature's Biodiversity to discover novel bioactive molecules and enzymes, which find application in the clinical trajectory and in biotechnology. 

Microbial Sciences contributes to the IBL research themes in the following ways:

Bioactive molecules: Microbial Sciences' contribution to the Bioactive Molecules research theme is to discover new bioactive molecules and enzymes and unravel their mechanisms of action, regulatory networks, and the (bio)synthetic pathways required for their production.

At the most fundamental level, all biological phenomena are driven by the coordinated activity of molecules of varying size and complexity. IBL researchers working in the theme area Bioactive Molecules take a molecular level approach to understanding and addressing key biological challenges.

As relates to human health, we focus on the identification and development of new, naturally inspired compounds to address: 1) infectious disease, with a specific focus on antibiotic resistance; 2) various cancers; and 3) inflammatory diseases. In addition, the potential for bioactive molecules, both small and large (i.e. enzymes), to be used in important industrial sectors such as agriculture and biotechnology represents another major focus area of this research theme.

The institute houses state-of-the-art infrastructure offering the capacity to screen for biologically active compounds from various sources (i.e. natural product extracts and small molecule libraries). In addition, the application of molecular biology and synthetic chemistry provides access to novel biomolecules with new properties. A large number of the projects conducted within the bioactive molecules theme are carried out as public-private partnerships between our scientists and researchers from various biotechnology and pharmaceutical companies. In this regard, we are always open to exciting proposals for research collaborations.

Development & Disease: Microbial Sciences'contribution to the Development & Disease research theme is to perform world-class research to understand cellular morphogenesis, growth, development and virulence of microbes.

We gain insights into the structure and function of microbial cells by a multidisciplinary and complementary approach based on our strong expertise in genetics, biochemistry, bioinformatics and state-of-the-art imaging techniques.

The microbial cell biology group of the IBL participates in the Centre for Microbial Cell Biology (CMCB), which unites the microbial cell biology expertise of the Leiden region.

Biodiversity & Evolution: Microbial Sciences' contribution to the Biodiversity & Evolution research theme focuses on understanding how bacteria sense and respond to their environment, and how bacterial diversity and evolution is influenced by cooperative and antagonistic interactions taking place between microbes.

Our experimental studies examine the chemical ecology of Streptomyces, the evolution of antibiotic production and resistance in nature and in bacterial pathogens, the origin of complex cells and the evolution of multicellularity, among other topics.

Host-Microbe Interactions: Microbial Sciences' contribution to the Host-Microbe Interactions research theme is to investigate how beneficial or disease-causing microbes associate and interact with their host.

Our research ranges from work on the molecular mechanisms underlying diseases caused by pathogenic bacteria and fungi to the interactions between beneficial bacteria and their plant hosts. To this end, we combine our strong expertise in microbiology, molecular biology, high-end imaging, computational biology and functional genomics. This knowledge can be used to generate microbial synthetic communities or new natural products for further application in medicine or agriculture.

The research group Science Communication and Society has been physically within the Institute of Biology (IBL) since 2012 and has become a formal part of the institute in 2018. The mission of this group is understanding how science communication works to improve the interaction between science and society.

Our research themes are:

• Bridging the gap between experts and the general public. One of the projects related to this topic is linking quantum technology to society. Moreover, multiple citizen science projects are performed and studied at our department, attempting to narrow this gap. In collaboration with the Hortus Botanicus, we study if participants will develop more attention for urban flora. We also conduct research on citizens collecting data about plastic pollution and animal rescue centers.
• Evaluating Science Communication. Science is portraited in the media in multiple ways. At our department, we use for instance content analyses to study science in the media, and we try to help people debunk misleading graphs in one of our research studies. Furthermore, we study how visitors experience the difference between real objects and replicas in science museums, and look at global perspectives on science communication. Lastly, in our project ‘Impact Lab’, we measure the impact of science communication and provide support and a toolbox for science communication organisers to measure their own impact.