Projects and grants

Does convergent evolution of molecular phenotypes shape immune responses in birds?

Goal: Compared to others, immune genes show increased coding sequence variation between species. Yet, how this variation affects diversity in immune defences is still unknown. While some species remarkably differ in their immune responses to pathogens, others are similar, but based on genomic data we cannot presently predict the differences in susceptibility to diseases. We propose that through revealing molecular convergent (parallel) evolution we can gain insight into functional genomic variation, advancing phenotypic predictions. We will test this hypothesis in inflammatory immune traits where we predict strong convergence, and focus on birds, a vertebrate taxon evolving in parallel to mammals. Our pilot data support all our predictions, suggesting potential of this project.

Principal investigator: Vinkler M.

Grantor: Czech Science Foundation

Duration: 2024-01 to 2026-12

Grant number: P303/24-12477S

Immunological mechanism of host evolutionary adaptation to increasing virulence in a
novel avian pathogen

Goal: Despite their key importance for predicting the epidemiological trends in emerging diseases, the molecular mechanisms of animal immunity evolution in response to infectious diseases remain mostly unknown. In 1990s, a new strain of the bacterium Mycoplasma gallisepticum (MG), a horizontally transmitted, economically important pathogen of poultry, caused in the eastern United States an epidemic in a new host, a small songbird, the house finch (Haemorhous mexicanus). The infection causes inflammation of the periorbital lymphatic tissue (mycoplasma conjunctivitis). The epidemic has been gradually spreading westwards, resulting in some areas of the US in a local decline of up to 60% in house finch abundance. Now populations on the west coast of North America are also affected, while immunologically naive isolated populations still survive, for example, on the Hawaiian Islands. In areas of contact, MG exerts strong selection pressure on its host. Recent results we obtained in collaboration with our American colleagues indicate that the house finch is gradually adapting to MG. Contrary to expectations, however, the birds increase their tolerance to infection, not resistance as predicted by the arms-race model. Therefore, populations adapted to MG suffer less from the disease (develop less skin lesions) at the same bacterial loads. In coevolution, the pathogen responds to this with stronger virulence, which contributes to its transmission. Our American colleagues have access to house finch individuals from different populations, and also viable historical isolates of MG (from the 1990s as well as recent) available for infection experiments. This is a unique host-pathogen model system that allows us to describe the general immunological mechanisms of the host evolutionary adaptation to a new, highly virulent disease. This focus is now key to future development in epidemiology of infectious diseases. The aims of our project are:
1) To describe the temporal dynamics of gene expression changes during mycoplasma conjunctivitis in the house finch, using transcriptomic data from conjunctiva and other tissues.
2) On the basis of these findings, create a sterile immunological model of the disease, which we will use to identify the key regulatory genes responsible for the tolerance adaptation to MG.
3) To experimentally verify the immunological effects of knocking down the key candidate molecules regulating the strength of conjunctivitis in the finches.
4) To map the variation in sequence and expression of selected
inflammation-regulating genes among the populations of house finch differing in their coevolutionary histories with MG (Virginia, Iowa, Arizona, and Hawaii – a unique dataset is available for our research).
5) With the help of our experimental model, to determine the differences in the immune effects of single, chronic and repeated contact with the pathogen, which can strongly influence the outcome of the evolutionary interaction of the house finch with MG.

Principal investigator: Vinkler M.

Grantor: Czech Ministry of Education

Duration: 2024-03 to 2028-12

Grant number: LUAUS24184

Effects of microbiota composition on inflammatory immunity and clinical symptom occurrence in socioeconomically-relevant parrots 

Goal: Hundreds of thousands of parrots, the most common pet birds, are annually traded on large distances, bringing significant economic profit, but also biosecurity risks. Despite their high prices, compared to mammals, strikingly little attention is paid to parrot microbiological and immunological research that would allow improvements in avian veterinary medicine. This project aims at understanding the relationships between microbiota composition, inflammatory activity of immune system, and health-related physiological responses of the parrots. Using biodiversity-based interdisciplinary approach we will describe interspecific as well as intraspecific variation in microbiota composition, reveal genetic variation in immune-related genes, explore regulation of cytokine pathways modulating inflammation in parrots, and investigate the relationship between these traits and diagnostic traits commonly examined in veterinary practice. Thus, we will provide insights into avian host-microbiota interactions as well as scientific basis for resolving practical therapeutic challenges.

Principal investigator: Vinkler M.

Grantor: Czech Science Foundation 

Duration: 2019-01 to 2021-12

Grant number: P502/19-20152Y

Impact of neuroinflammation on brain development and learning in cognitively advanced birds

Goal: The rapid increase of mood disorders (e.g. depression) in human society is alarming. Insufficiency of present therapeutic approaches creates high demands on novel strategies to study factors affecting mood-related brain function. Neuro-immune interactions involved in neuroinflammation directly influence psychological processes including mood and cognition. Given their unique mental capacities and other physiological similarities to primates I suggest that passerine birds and parrots represent ideal models for advanced research in neuroinflammation and cognition (superior to rodents). The proposed interdisciplinary project will significantly improve our so far limited understanding of avian neuroimmunology. At transcriptomic, proteomic, neurohistological, and behavioural levels a newly formed team will describe effects of inflammation on neurogenesis and brain gene-expression changes in birds and their influence on avian ability to resolve tasks indicative of learning capacities and mood. Providing novel insight into the causalities between inflammation and brain cognitive function, this project will bring traditional zoological disciplines closer to practically applicable outcomes.

Principal investigator: Vinkler M.

Grantor: Charles University (Prague)

Duration: 2018-01 to 2020-12

Grant number: PRIMUS/17/SCI/12

Mapping of diversity in avian genomic resources available in the Czech Republic

Goal: The main goal of this project is to develop a methodological and material basis for animal genome annotation through description of diversity in avian genetic resources in the Czech Republic (domestic as well as free-living). The project is based on international collaboration and knowledge-transfer within the FAANG-Europe community and contributes to the development of European genomic resources awareness in general (open data). The aims are divided into three sub-tasks:
1) To develop the national collection of avian genomic samples (under ZCU genetic bank).
2) To create a new collection of RNA samples available for transcriptomic research.
3) To describe in selected genetic resources represented in these collections expression and sequence transcriptome variation using modern methods of RNA-seq and WTTS-seq in collaboration with international FAANG partners.

Principal investigator: Vinkler M.  

Grantor: Ministry of Education, Youth and Sports of the Czech Republic: Inter-Excellence 

Duration: 2018 to 2020 

Grant number: LTC18060

Biology of ageing: mechanisms and patterns of senescence in free-living birds

Goal: This project focuses on understanding the biology of ageing in a group of organisms characterized by high metabolic activity and relatively long lifespans: birds. By combining inter- and intraspecific approaches with both observational and experimental data, we will evaluate several key predictions of basic evolutionary hypotheses (mutational x optimality) proposed to explain the process of ageing and intra- or interspecific variation in the pace of senescence. Specifically, we will (1) describe the dynamics of senescence and intrinsic mechanisms behind ageing, (2) explain within-species variation in ageing patterns, and (3) explore the interspecific variation in ageing patterns across birds. The suitability of several new markers of ageing will be, for the first time, evaluated in free-living populations of animals. Our unique interdisciplinary approach will help to uncover evolutionary mechanisms underlying ageing processes in birds. The results from this project may also prove useful for understanding the process of ageing in other vertebrates, including humans.

Principal investigator: Albrecht T. 

Co-Principal investigators: Vinkler M., Syslová K., Cepák J. 

Grantor: Czech Science Foundation (Prague)

Duration: 2015-01 to 2017-12

Grant number: P506/15-11782S

BIOM: Biodiversity education centre Mohelský Mill

Principal investigator: Bryja J. 

Co-Principal investigator: Vinkler M.

Grantor: EEA Grants (Brussels)

Duration: 2015-01 to 2016-06

Grant number: EHP-CZ02-OV-1-025-2015

Pattern recognition receptor allelic diversity in domestic chicken breeds

Goal: In this project we aimed to investigate the genetic variability and evolution of innate immune receptor genes in Galloanserae birds and traditional breeds of the domestic chicken. We selected the genes to cover the most important groups of PRRs known in vertebrates: antiviral TLRs (TLR3 and TLR7), antibacterial TLRs (TLR4 and TLR5), antibacterial NLRs (NOD1) and antiviral RLRs (MDA5).

Principal investigator: Vinkler M. 

Grantor: Czech Science Foundation (Prague)

Duration: 2012-01 to 2014-12

Grant number: P502/12/P179

Student projects

Dynamics of gut microbiota composition in parrots and the effects of selected symbiotic bacteria on the host‘s clinical condition and behaviour

Goal: Parrots (Psittaciformes) are one of the most common avian groups kept in households, with captive individuals accounting for approximately half of their global population. However, they are also frequent patients of veterinary practitioners. The most common health issues in parrots include behavioural, gastrointestinal, and metabolic disorders. All of these disorders may be directly or indirectly (through gut-brain axis) related to the intestinal microbiota. Therefore, the research focused on interactions between the gut microbiota and the brain in parrots suggests significant potential for application. Yet, this topic has received almost no attention so far. Based on our preliminary data, inflammation induced in very young individuals can result in long-term behavioural changes that are detectable even in adulthood. The proposed project combines metabarcoding with cultivation and in vivo experiments and has the following aims: (1) to describe the long-term dynamics of gut microbiota composition and the stability of candidate bacteria in a semi-wild population of budgerigars; (2) to describe changes in gut microbiota composition and the abundance of candidate bacteria in budgerigars in a model of subclinical chronic inflammation that causes long-term behavioural changes; (3) to isolate and cultivate the selected candidate bacterium directly from the oral cavity of parrots and to test its properties necessary for veterinary application in a pilot in vivo experiment.

Principal investigator: Marková K.  

Mentor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2024-03 to 2026-12

Grant number: 96924

The avian inflammasome: gene evolution, expression, and interactions with microbiota following immunological challenges

Goal: Emerging zoonotic infectious diseases represent an important threat to human health. Birds that can transmit these diseases are widespread in anthropogenic habitats. While they can transmit pathogens on large distances, they can also have a positive effect on human immunomodulation (One Health concept promoted by WHO). In this project, we focus on the interactions of microbes with passerine and parrot inflammasome components, a key step in determining the infection outcome. We will 1) describe the evolution of avian inflammasome genes (selection pressures on adaptive features of the genes), 2) characterise the patterns of their expression during the targeted immune responses (condition of acute and chronic inflammation) and 3) reveal links between the variation in these genes (sequence and expression) and distribution of avian bacterial symbionts. This project will importantly contribute to finding the knowledge base on the diversity of host-microbe interactions, which is essential for future predictions of the host resistance to various infectious diseases and their transmission to humans.

Principal investigator: Melepat B.  

Mentor: Vinkler M. 

Grantor: Start programme, Charles University (Prague)

Duration: 2021-04 to 2023-03

Grant number: START/SCI/113

Effect of heavy metal contamination on gastrointestinal microbiota in great tit (Parus major)

Goal: Due to human anthropogenic activity, a considerable amount of pollutants, including heavy metals, is emitted into the environment. As the toxic elements of this group (As, Cd or Pb) are dangerous even at low concentrations, their geographical distribution and negative impact on organisms are monitored. The heavy metals are ingested into the body with the diet, and therefore can affect the gastrointestinal microbiota, which contributes with a variety of functions to the host´s health. Although birds represent potentially valuable bioindicators of environmental quality, virtually nothing is presently known about the effects of heavy metal contamination on composition of their microbiota. This project aims to 1) clarify the relationship between the gastrointestinal microbiota and heavy metal contamination in great tits; 2) experimentally test the effects of sublethal doses of cadmium on the gastrointestinal microbiota composition and other health and condition-associated traits in zebra finches; 3) clarify the patterns of cadmium deposition across variety of tissues. This project will enable us to understand the impact of pollution on aspects of health of the free-living animals that have not been studied so far. 

Principal investigator: Krajzingrová T.  

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2021-03 to 2023-12  

Grant number: 297121

Geographic variability of heavy metal contamination and its effects on health and aging in the great tit (Parus major

Goal: Heavy metals, which are released into environment as a consequence of human activity, are harmful for human and animal health. Despite the fact that some elements (Fe, Cu, Zn) can be important in lower concentrations, others (Pb, Cd, As) are toxique at any concentration. Degree of contamination with heavy metals in animals varies based on locality or variety of heavy metal which causes pollution. Free-living animals may serve as indicator of this contamination, regional differences or changes in accumulation of heavy metals. This project will be first which will use blood samples of great tits from different localities in the Czech Republic and Europe to bioindicate variability of heavy metal loads. Moreover, the effect of heavy metals on physiology during aging will be studied on samples taken during already completed project. Due to lack of experimentally obtained evidence of influence of heavy metals on bird health, trial will be part of project to clarify effect of sub-lethal doses of cadmium on metallothionein expression and hematology. This project will help to understand regional differences in burden of heavy metals and their impact on these organisms. The transferability of knowledge to humans and livestock will raise zoological-ecological research of wildlife at public. 

Principal investigator: Krajzingrová T.  

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2018-03 to 2020-12  

Grant number: 1626218

Microbiome of bird egg in early and late embryogenesis: impact of experimental in ovo probiotics administration on establishment of microbiota and gene expression of immune genes in birds

Goal: In birds, bacteria colonize gastrointestinal tract in embryonal development. The interaction between gut microbiome and immune system in this period is crucial for adjusting immunity. To explain bacterial colonization of bird egg two hypotheses have been proposed: (1) vertical transfer of microbiome from mother to egg in oviduct and (2) trans-shell migration of bacteria invading egg during laying and incubation period. How important are these mechanisms for establishment of gut microbiota is still poorly understood. The main aims of this project are by using NGS sequencing of bacterial 16S rRNA to describe bacterial taxonomic diversity of egg white immediately after laying and to evaluate its impact on establishment of gut microbiota in late embryogenesis as well as on gene expression of immune genes (applying RNAseq and RT-qPCR) in two model species. In the first year, we will describe natural gut microbiome (descriptive approach) and then we will apply manipulative approach (the impact of in ovo administration of probiotics) in chicken (Gallus gallus) and in the second year in great tit (Parus major). The results of our project will improve our understanding of primary establishment of gut microbiota and its effect on immunity, but it may also provide practically applicable outcomes. 

Principal investigator: Těšický M.  

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2017-03 to 2019-12  

Grant number: 1158217

Sequence and expression variability in chicken antimicrobial peptides

Goal: Antimicrobial peptides (AMPs) belong to essential components of animal immune system. AMPs allocated into avian eggs in maternal oviducts provide anti-­pathogen protection to developing embryos. Although eggs of the domestic fowl (Gallus gallus) serve as a nutritious food source, their consumption is associated with increased risk of pathogen infections. Biosecurity of eggs can be improved by selection on natural disease resistance in chickens. Unfortunately, modern egg-­layers have undergone intense artificial selection for high productivity, which reduced their genetic variability in general and variation in immunologically relevant genes in particular. In contrast, rarely studied ancient chicken breeds, formed by region-­specific artificial as well as natural selection, are genetically highly diversified. Goals of our project are to map genetic variability in candidate AMPs in ancient and modern chicken breeds, estimate functional significance of this variation, measure differences in AMP expression in maternal oviducts in distinct breeds, and analyse AMP concentrations and bacterial-­killing activities in egg whites originating from different breeds. Recent research has revealed the importance of genetic and expression variability in AMPs for variation in anti-­parasite resistance. The results of our project will improve understanding of the evolution of local immunological adaptations in chickens and may also provide practically applicable outcomes. 

Principal investigator: Bílková B  

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2015-03 to 2017-12  

Grant number:  275715

Phylogeny of domestic fowl breeds and gene flow between them 

Goal: Domestic chicken (Gallus gallus) is an essential model for avian biological research and an important domestic species. The research in this species is mainly focused on general investigation in avian biology (immunological and physiological research in inbred lines) or on a phylogenetic comparison of wild populations of junglefowl with modern breeds. Although ancient breeds derived from locally farmed rural fowl represent a valuable source of novel information for evolutionary research, presently they escape much attention. One of the important questions is, how much genetically diverse these breeds are. Currently we completely miss any idea about their phylogeny and interbreed variability in neutral and selected loci. In the present project we will focus on evaluation of phylogenetic relationships among 20 ancient and 10 modern chicken breeds kept in the Czech Republic. On a sample of 400 individuals we will compare the interbreed diversity at 2 neutral markers, 6 immune genes and 6 genes encoding exterior characters. These data will be used to determine the extent of gene flow between the breeds for different categories of genes. We assume that the practice of „reviving blood“ and the subsequent artificial selection allows greater flow in immune genes than genes responsible for exterior traits.

Principal investigator:  Chudárková (Šmídová) A., Buchtová L.  

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2014-03 to 2016-12  

Grant number: 504214

Trans-species polymorphism in selected genes of innate and acquired immunity in tits (Paridae)

Goal: Better understanding of host-parasite co-evolution is important not only from academic perspective (evolutionary biology), but also for practical reasons (epidemiology and biomedicine). Free-living animals in which natural selection is still acting are essential models for investigation of evolutionary adaptations in immunity. The trans-species polymorphism (TSP) concept proposes that in related species balancing selection maintains advantageous alleles allowing there transfer from ancestor species to several descendant species. In this project we aim to test this hypothesis by analysing sequences of four immune genes in population samples of 21 tit species (ca. 1/3 of the world tit species richness). As target genes we have chosen two Toll-like receptor genes (TLR4 and TLR5) representing innate immunity and two Major histocompatibility complex genes (MHCI a MHCII) representing acquired immunity. These genes encode immunologically important molecules that are involved in direct physical contact with pathogen structures. As they allow recognition of particular pathogen types, we may assume that these genes are under strongest pathogen-mediated selection. The goal of this project is to describe inter- and intraspecific variability in binding regions encoded by these genes, to identify positions and evolutionary lineages under positive selection, to detect footprints of recombination among alleles and to evidence the TSP. 

Principal investigator: Velová (Bainová) H. 

Guarantor: Vinkler M. 

Grantor: The Charles University Grant Agency 

Duration: 2014-03 to 2016-12  

Grant number: 540214

Description of the structure and population polymorphism of Toll-like receptor 4 in Great tit (Parus major) with implication to its association with individual condition, health and ornamentation

Principal investigator: Vinkler M. 

Guarantor: Albrecht T.

Grantor: Charles University Grant Agency (Prague)

Duration: 2009-01 to 2011-12

Grant number: 44809

Signal function of the carotenoid and melanin ornamentation in the Great tit (Parus major)

Principal investigator: Vinkler M. 

Guarantor: Albrecht T.

Grantor: Charles University Grant Agency (Prague)

Duration: 2007-01 to 2008-12

Grant number: 127507