Laboratory of Environmental genomics
The majority of Earth’s biodiversity is microscopic and cannot be kept in permanent cultures. However, our knowledge of life is based on extensive exploitation of few either macroscopic (Arabidopsis, Oryza, Drosophila, Caenorhabditis, rat or Xenopus…) or cultivable unicellular (Saccharomyces, Neurospora, Chlamydomonas…) models representing only a small fraction of true diversity. Laboratory of environmental genomics was founded in March 2013 and its main goal is to characterize diversity, ecological role and metabolic potential of important/interesting unicellular eukaryotes not available from cultures using the power of the next-generation sequencing and bioinformatics.
Research projects
Investigate the role of JH during mosquito development.
Hypothesis: in the absence of JH, MF is able to activate regulatory pathways that control development and metamorphosis. Transcriptomic analysis of whole larvae from two null mutant lines and wild-type mosquitoes are currently being used to identify a set of differentially expressed genes that will be tested for function through a combination of RNAi and physiological experiments.
We aim to understand how the absence of JH affects reproduction.
JH regulates nutritional homeostasis, and the absence of epoxidized JH leads to loss of reproductive capacity in female and male mosquitoes. Transcriptomic analysis of ovaries from adult females of our mutant line and wild-type mosquitoes are currently being used to identify a set of differentially expressed genes that will be functionally tested.
Investigate the regulation of JH biosynthesis in the corpora allata gland of mosquitoes (CA).
We are combining microscopic imaging and various molecular and biochemical techniques to investigate the role and mechanism of action of various factors that control the activity of CA.
Trajectories of genome evolution in convergently evolving insect lineages
Organisms often evolve similar adaptations to similar environments in the process of convergent evolution, indicating that the trajectory of phenotypic evolution is amenable to predictions. Whether the genomic trajectories of convergent organisms are parallel - and thus predictable in principle - is unclear due to the scarcity of genomic evidence from convergent organismal groups. To answer these questions, we are using a model system consisting of rove beetles (Staphylinidae: Aleocharinae) and scuttle flies (Phoridae) that adapted more than twenty times repeatedly to live in symbiosis with termites. Using phylogenetics, comparative genomics, transcriptomics, and microtomographic reconstructions of phenotypes, we will infer the extent, the timescale, and the hierarchical level of genome sequence evolution at which parallel patterns of genome evolution accompany the evolution of convergent adaptations.
Research in collaboration with Tom Bourguignon (OIST, Japan) and Taisuke Kanao (Yamagata University, Japan).
Funding: 5-year research grant JUNIOR STAR GAČR from the Czech Science Foundation(25M CZK ~ 1M EUR, 2023-2027).
Termite phylogenetics
Termites with ~ 3,100 described species represent a modestly diverse group which, however, reached a global ecological impact during the estimated ~ 140 millions of years since the inferred diversification of the last common ancestor of all living termite species. To reconstruct the diversification of termite lineages we built phylogenetic hypothesis using a range of molecular genetic markers, including mitochondrial genomes, nuclear protein-coding gene orthologs, and nuclear ultra conserved elements. These backbone phylogenetic trees allowed us then to infer the shifts in symbiotic relationships within termite guts (Buček et al. 2019), or the historical biogeography of termites and their dispersal potential (Buček et al. 2022, Wang et al. 2019, Wang et al. 2022).
Research started in the lab of Tom Bourguignon (OIST, Japan) and Jan Šobotník (CULS, Czechia).
Evolution of defense in termites
One of the likely key adaptations that led to the evolutionary success of termites is defense. While some termite workers evolved remarkable self-sacrificial chemical defensive strategies, the principal termite colony caste responsible for active defense are the soldiers. Termite soldiers typically combine their capacity to produce chemical secretions (Jirošová et al. 2017, Bourguignon et al. 2016) and mechanical weapons in the form of their mandibles (Beránková et al. 2022). One remarkable mandibular defense strategy - so called mandibular snapping - presumably evolved many times independently in termites. In this strategy, soldiers of some termite species evolved mandibles that lost the biting ability and instead adapted into springs that can deliver a lethal strike to insect competitors of termites. Remarkably, this highly derived mandibular strategy apparently evolved multiple times convergently. Currently, we are conducting a comparative evolutionary study across termite lineages to uncover the evolutionary trajectories that lead to mandibular snapping.
Research started in the labs of Tom Bourguignon (OIST, Japan) and Jan Šobotník (CULS, Czechia).
Funding: 2-year research grant KAKENHI from the Japan Society for the Promotion of Science (2023-2024).
Illuminating the interactions between nitrification and methane oxidation and the ensuing ecological impacts
Financial suppport: Czech Science Foundation (GACR); Duration: 2021-2025
Principal Investigator: Anne Daebeler
Team members: Magdalena Wutkowska, Anna Prokhorova, Justus Nweze, Renata Kruzikova
Nitrifiers and methanotrophs are microbial guilds responsible for aerobic transformation of reactive nitrogen and oxidation of methane, respectively. Both processes are fundamental ecosystem functions linked to nutrient cycling and global change. We hypothesize that interactions between these two guilds substantially contribute to the modulation of process rates. However, such interactions have hardly been investigated. The proposed line of research will expose the cause and nature of interactions between nitrifiers and methanotrophs and quantify their ecological impact. The project will employ a unique combination of multidisciplinary techniques, i.e. next generation sequencing, stable isotope incubations with integrated approaches of metagenomics and metatranscriptomics, single cell sorting, and metaproteomics with synthetic microbial consortia. Collectively, these approaches are poised to gather a deep understanding of the links between carbon and nitrogen cycling to eventually be able to predict and mitigate climate change and protect Earths ecosystems.
The project will resolve interactions between nitrifiers and methane oxidizers, quantify their ecological implications, and develop models for predictions. It will fill knowledge gaps on microbial ecogenomics and -physiology, and isolate new organisms.
TIMPAOMP project - The IMPortance of Anaerobic Oxidation of Methane in Peatlands
Financial suppport: Czech Science Foundation (GACR); Duration: 2023-2025
Principal Investigator: Vojtech Tlaskal
Team members: Renata Kruzikova
Ecosystem management of natural wetlands is an important tool of human land use practises that often have untargeted impacts on greenhouse gas (GHG) emissions such as methane. Systems such as northern peatlands are very sensitive to management practises and at the same time have the potential to release large amounts of GHGs due to their large storage of organic matter. As a result of practised clear-cutting of peatland forests the water table rises. At the same time, anoxic conditions in peat are expanding, creating a new niche for microbial greenhouse gas producers, but also for anaerobic methanotrophs that depend on substantial methane production and the presence of oxidised electron acceptors. There is a lack of knowledge about the proportion of anaerobically oxidised methane, the identity of the bacteria and archaea that carry out such process, their electron acceptors and nitrogen sources in peatlands. Filling these knowledge gaps, which are urgently needed to improve ecosystem models and reduce GHG emissions, is the subject of this project.
Side effects of transgenic plants
The aim of this project is to evaluate the effects of genetically modified maize on the biotic components of an agroecosystem. The study will be conducted with maize varietiety MON 88017, which tolerate the herbicide glyphosate and are resistant to rootworm infestation. This pest, which was introduced into the EU from the USA, is spreading rapidly and has taken over some of the country's maize-growing areas. Current chemical and biological control methods are unsatisfactory, so genetically modified maize is being considered as an alternative, provided no adverse effects on non-target organisms are identified. Herbicide-tolerant plants dominate the market for genetically modified plants, but their cultivation is not yet permitted in the EU.
PI: Oxana Skoková Habuštová
Innovation of integrated potato protection against the Colorado potato beetle based on new knowledge of genetic and biological characteristics
The project is carried out in cooperation with the Czech University of Agriculture in Prague, the Research Institute of Plant Production in Prague, the Potato Research Institute in Havlíčkův Brod and the Potato Farm in Havlíčkův Brod and is funded by the National Agency for Agricultural Research (NAZV).
The project solves the problem of integrated protection against the Colorado potato beetle in a way that has not yet been solved in the Czech Republic.
The aim of the project led by Biology Centre Institute of Entomology (ENTÚ) is to design a system for the effective cultivation and development of a mycoinsecticide formulation based on the already laboratory-tested strain of the entomopathogenic fungus (EPF) Isaria fumosorosea CCM 8367 and/or newly isolated strains of EPF Bb8 and to verify its efficacy in field trials. From this point of view, the laboratory investigation of the synergism of EPF and entomopathogenic nematodes (EPN) is absolutely necessary. Research and clarification of the physiological background of the supporting effect of the adipokinetic hormone (AKH) on the efficacy of insecticides will provide new insights.
PI: Oxana Skoková Habuštová
Integrated protection against vectors of viral diseases in seed potatoes and other crops
The project is carried out in cooperation with the Czech University of Agriculture in Prague, the Research Institute of Plant Production in Prague, the Potato Research Institute in Havlíčkův Brod and the Potato Farm in Havlíčkův Brod and is funded by the National Agency for Agricultural Research (NAZV).
The project deals with the regulation of potato virus vectors in the Czech Republic, such as peach aphids, hop aphids and buckthorn-potato aphid. The project offers a very comprehensive solution for the control of aphids. Due to the increasing resistance of aphids to the preparations previously used in Europe, a change of active ingredients is recommended.
The aim of the project led by Biology Centre Institute of Entomology is therefore to develop and test the efficacy of new biological preparations against viral vectors based on EPF such as Lecanicillium sp., Beauveria bassiana, Metarhizium anisopliae, Isaria sp. and Nomuraea rileyi, testing secondary metabolites from EPN, environmentally friendly botanical pesticides that also have anti-feeding and repellent effects. The project can thus support the selection and registration of new effective preparations.
PI: Oxana Skoková Habuštová
Do social insect impacts on soil properties maintain tropical plant diversity in the face of anthropogenic habitat change?
Using a combination of field surveys, experimental manipulations, and individual-based
modelling, we will quantify the contribution of soil-dwelling social insects in maintaining tropical
rainforest tree diversity via impacts on soil properties in the face of anthropogenic habitat
change
Funding 2024-2026 (GAČR), PI: Tom Fayle
Endosymbionts of trypanosomatids and diplonemids
Although most trypanosomatid flagellates do not harbor endosymbiotic bacteria, members of the genera Angomonas, Strigomonas, Novymonas and Kentomonas do so. They acquired their endosymbionts by at least two independent events and seem to obtain from them various macromolecular precursors and vitamins. Diplonemids (for more information see other project abstract) contain numerous endosymbionts obtained by multiple independent (and probably repeated) acquisitions, but nothing is known about their metabolic interaction with their hosts. However, we predict that in both trypanosomatids and diplonemids, endosymbiotic bacteria have significant impact on their hosts, including their behavior, life cycle progression and ecological functions.
We are dissecting the relationship between the eukaryotic host and its bacterial symbiont using protein tagging and functional genomics. We have already identified in Novymonas a protein that is critical for the intracellular distribution of bacteria. In diplonemids, we succeeded to experimentally remove endosymbionts from the host cells and reinfect them. We believe that the protist-bacterium systems that are established in our laboratory will allow us fine dissection of their intricate relationships.
Why is there such high diversity of chemical defences? The role of insect herbivory in promoting chemical diversity in willows
Chemical diversity of plant defences is a major driver of insect-plant interactions. Answering the question “Why is there such high diversity of chemical defences?” is thus crucial for understanding key ecological processes that shape composition and diversity of insect-plant assemblages. Our aim is to unravel the mechanisms by which chemical diversity evolves. To achieve this, we use ecologically dominant and diverse willows as a model genus. We contrast chemical defences and herbivore communities of allopatric and sympatric willow species. This will help us to show how the exposure to local pools of herbivores promotes the diversity of willow defences and leads to their divergent evolution (Figure 1). Furthermore, we use greenhouse experiments to dissect how the overall diversity of chemical defences arises from individual insect-plant interactions and their specificity. Only such an integrative approach using field surveys, manipulative experiments, and cutting-edge analytical methods can demonstrate how the diversity of defensive secondary metabolites is generated.
Figure 1. Evolution of defences along the phylogeny of Ficus (A), Salix (B), and Macaranga (C) based on the data from Segar et al. (2017); Volf et al. (2015); Volf et al. (2018) and our preliminary results. Left-oriented columns suggest divergence.
We combine field sampling with manipulative greenhouse experiments to achieve our goals.
Population genomics of speciation and adaptation in parasites
We study genomic imprints of speciation and adaptation processes in two parasitic species, the tapeworm Ligula intestinalis and the bedbug Cimex lectularius. Despite differences in their ecology and evolution, both species show wide geographical range and many oportunities for emergence of specific adaptations (associated with host specificity in the tapeworm, or with insecticide resistance in the bedbug). Using SNP profiling, transcriptomis and WG sequencing we're evaluating the impact of geographic structuring and gene flow on adaptive processes in the two parasites (P.I.: J.Štefka).
Commensal Intestinal Protist: A Part of a Healthy Microbiome?
In recent years, it has become evident that the intestinal microbiome plays a crucial role in our health. However, it is not just bacteria that matter—benign helminths and intestinal protists also play a significant role, becoming an essential part of an optimally functioning gut ecosystem.
One fascinating example is the intestinal protist Blastocystis. This organism was, until recently, primarily associated with severe inflammatory conditions, such as Crohn's disease or irritable bowel syndrome. However, more recent scientific studies, including those focused on healthy individuals, suggest that Blastocystis is more likely a commensal organism—one that lives in harmony with our bodies (e.g., Lhotská et al., 2020, Front Cell Infect Microbiol; Šejnohová et al., 2024, One Health). Despite these findings, comprehensive experimental studies are still lacking to fully elucidate its overall impact on host health, including its effects on the immune system and the composition of the gut microbiome.
To unravel this mystery, we developed a rat model (Růžková et al., 2018, Exp Parasitol), which has already partially demonstrated the beneficial effects of Blastocystis colonization on intestinal inflammatory diseases under certain conditions. We are now focusing on a detailed investigation of how the Blastocystis genome changes during its colonization of the host's gut, which will help us better understand the complex interplay between the gut ecosystem, this protist, and the host's immune system.
Our work doesn't stop here—we are currently engaged in additional projects exploring the role of Blastocystis in human health, in collaboration with clinical institutions.
If you are interested in this project, please contact RNDr. Zuzana Pavlíčková, Ph.D. (zuzana.lhotska@paru.cas.cz).
Intestinal Worms: Surprising Protectors of Our Health
Helminths, commonly known as worms, are often seen as unwanted parasites, but their role in our bodies is far more complex and intriguing. Over hundreds of millions of years of co-evolution with humans and other hosts, these tiny creatures have developed incredibly sophisticated ways to influence our immune system. Rather than merely surviving, helminths actively manipulate the host’s immune response to prevent the inflammation that could destroy them. Although they can be pathogenic under certain conditions, it is becoming clear that the complete disappearance of these organisms from our environment may have serious consequences for our health.
Studies worldwide show that the absence of helminths in the human body is associated with a dramatic increase in chronic inflammatory diseases (CIADs)* in developed countries. These diseases, such as Crohn’s disease, multiple sclerosis, and various allergies, share common risk factors that are particularly prevalent in developed societies.
Recent research on the gut microbiome suggests that reintroducing helminths into the gut ecosystem could be a revolutionary step in treating CIADs. This approach, known as helminth therapy, uses controlled exposure to non-pathogenic or mildly pathogenic worms to activate anti-inflammatory immune responses. Our laboratory is focused on testing the rat tapeworm (Hymenolepis diminuta), which is known for its typically asymptomatic presence in the host organism. Our recent studies have shown that this tapeworm can significantly reduce intestinal inflammation under certain conditions.
Helminth therapy is on the rise, and we are on the brink of new discoveries. To fully understand the interactions between host and helminth, we are investigating how diet composition and other factors affect the efficacy of H. diminuta in treating inflammatory diseases. This tapeworm is emerging as one of the most promising candidates for therapeutic use.
Our research is conducted in collaboration with William Parker’s laboratory at Duke University in the USA, where scientists specialize in studying the effects of H. diminuta on neuropsychiatric disorders, including autism.
If you are interested in this project, please contact MVDr. Kateřina Jirků, Ph.D. (pomajbikova@paru.cas.cz) or RNDr. Milan Jirků (jirku@paru.cas.cz).
*Chronic inflammation-associated diseases (CIADs): refers to a broad class of diseases and conditions caused by chronic inflammation. Accompanied by immune dysregulation, this group of diseases and conditions includes allergies, a range of autoimmune conditions, some neuropsychiatric disorders, and some digestive diseases.
Protists and Human Health: A New Perspective on an Old Coexistence
Scientists have recently discovered that tiny protists residing in our intestines play a crucial role in the health of not only animals but also humans. Unlike the well-known bacteria, intestinal protists remain somewhat of a mystery, especially when it comes to their diversity in Western societies (Lukeš et al., 2015, PLoS Pathog).
For a long time, it was believed that protists were dangerous parasites that needed to be eradicated. However, we now know that many of these organisms are a natural and essential part of a healthy gut microbiome. For example, protists like Blastocystis spp. and Dientamoeba fragilis are much more common in healthy individuals than in those suffering from chronic inflammatory bowel diseases (Lhotská et al., 2020, Front Cell Infect Microbiol; Jirků et al., 2022, Int J of Mol Sci).
Another interesting discovery shows that the presence of these beneficial protists is associated with greater diversity in gut bacteria—a key factor for our health. Our project focuses on monitoring these protists, such as Blastocystis, Dientamoeba, Giardia, Entamoeba, and others, in healthy individuals. Additionally, we are investigating possible transmissions between people and their pets, which could reveal new and important connections.
One of the surprising findings of our research concerns the occurrence of Giardia intestinalis in the healthy population. This protist is commonly detected in patients with clinical symptoms of giardiasis. However, our study revealed that 7% of healthy volunteers in the Czech Republic are asymptomatic carriers of this parasite, which we identified using a sensitive qPCR diagnostic method (Brožová et al., 2023, Emerg Microbes Infect).
Given that protists have been an integral part of the human gut ecosystem throughout evolution, it is time to reconsider their role in the modern world.
If you are interested in this project, please contact RNDr. Kristýna Brožová (kristyna.brozova@paru.cas.cz)
Intestinal Protists in Non-Human Primates
Our laboratory has recently begun focusing on the epidemiology of intestinal protists in non-human primates within zoological gardens. We are particularly interested in protists such as Blastocystis sp., Dientamoeba fragilis, and Giardia intestinalis, which play a key role in the gut microbiome (Šejnohová et al., 2024, One Health). These organisms are gaining increasing attention from scientists, as it becomes evident that their presence can have significant impacts on the health of their hosts, not only in primates but also in the broader context of animal and human populations.
If you are interested in this project, please contact MVDr. Kateřina Jirků, Ph.D. (pomajbikova@paru.cas.cz) or RNDr. Milan Jirků (jirku@paru.cas.cz).
AlgaRePo: Revitalization of phytotoxic soils using cyanobacteria and algae
Technology Agency of the Czech Republic (TA ČR), co-principal investigator, 2024-2026
The goal of the project is to design and apply innovative biotechnology for revitalizing phytotoxic soils (e.g. coal mining dumps) based on the use of specific cyanobacteria and microscopic algae, or their consortia. When selecting the strains, emphasis will be placed on natural extremotolerant representatives. The selected strains will be applied in the locality of interest, where they will form a biocrust and thereby improve the physical, chemical and biological quality of the soil. It will also serve to retain water in the landscape, thereby enabling further settlement and revitalization of the originally phytotoxic soil. These resistant strains growing on soil will also be able to grow in water, and therefore they will be used for remediation of waste water and water habitats.
Project of the Czech Technology Agency within the Environment for Life Programme: SS73020005 Integrated Monitoring of PArasites in Changing EnvironmenTs
Principal investigator: prof. RNDr. Tomáš Scholz, CSc.
The aim of the project: In line with the "Environment for Life" programme, the proposed project represents a significant methodological and professional innovation in the assessment of the state of biodiversity, in particular of freshwater fish parasite communities, which are an integral part of ecosystems and are also very sensitive bioindicators of their changes. With the participation of nine leading centres from seven of the most developed countries in Europe, the project will have a pan-European scope and will contribute to improving the quality of life not only in Europe but also in a global context. The use of new approaches, i.e. the best available techniques (BAT - eDNA metabarcoding, Next Generation Sequencing - NGS, mitogenomics), will greatly facilitate the monitoring of biodiversity changes, including the prediction of potential impacts of climate change on aquatic ecosystems and the subsequent design of strategic biodiversity conservation measures (conservation element).
Project duration: 01/2024-12/2026
Systems biology approaches to better understand disease vector lifecycles
(a) I. ricinus transmits Borrelia burgdorferi (Lyme disease) and several other arboviral diseases via the salivary glands. We used massive de novo sequencing to characterize the transcriptional dynamics of the salivary and midgut tissues of nymphal and adult I. ricinus at various time points after attachment on the vertebrate host (Kotsyfakis et al., 2015, Sci Rep. 5, 9103). A number of gene family members showed stage- and time-specific expression, with 34 candidate histone-modifying proteins suggesting epigenetic control. Midgut transcriptome analysis revealed several enzymes associated with protein, carbohydrate, and lipid digestion, transporters and channels associated with nutrient uptake, and immune-related transcripts including AMPs.
(b) We identified hemocyte transcripts from semi-engorged female ticks by mass sequencing a hemocyte cDNA library and annotating immune-related transcripts based on their hemocyte abundance and their ubiquitous distribution (Kotsyfakis et al., 2015, PLoS Negl Trop Dis. 9, e0003754). 327 transcripts were significantly overexpressed in the hemocyte libraries, including those coding for scavenger receptors, AMPs, pathogen recognition proteins, proteases, protease inhibitors, lipid metabolism, and immune function. The coding sequences deposited to GenBank significantly increased the publicly available dataset now supporting biochemical, pathophysiological, and translational studies. These gene expression analyses (Chmelař et al., 2016a, Trends Parasitol. 32, 242–254) represent a milestone in the field, and the application of quantitative proteomics to ticks with unknown genomes has provided deeper insights into the molecular mechanisms underlying tick-host-pathogen interactions.
Disease vector-host interactions
(a) Given that tick salivary secretions are critical to the success of the tick transmission lifecycle, we systematically reviewed known interactions between tick saliva/salivary gland extracts and the vertebrate immune system (Kotál et al., 2015, J Proteomics. 128, 58–68). This allowed us to promote the hypothesis that tick salivary protein family members display redundancy and pluripotency in their action on host immune responses (Chmelař et al., 2016b, Trends Parasitol. 32, 368–377). This concept is observed in the three major groups of protease inhibitors secreted into saliva: Kunitz inhibitors (anti-hemostatic) and serpins and cystatins (anti-hemostatic and immune system modulators) (Chmelař et al., 2017, Front Cell Infect Microbiol. 7, 216). We described and functionally and structurally characterized the novel immunomodulatory cystatin, Iristatin, in the salivary glands of feeding I. ricinus ticks (Kotál et al., 2019, Cell Mol Life Sci. 76, 2003–2013). Purified recombinant Iristatin inhibited the proteolytic activity of cathepsins, diminished pro-inflammatory cytokine production by different immune cell populations, and inhibited OVA antigen-induced CD4+ T cell proliferation and leukocyte recruitment in vivo. These pluripotent actions may be exploitable as an immunotherapeutic.
(b) We also described novel arthropod miRNAs in I. ricinus salivary glands and saliva (Hackenberg M et al., 2017, RNA. 23, 1259–1269). De novo prediction yielded 67 miRNAs, of which 35 were not present in miRbase, potentially of exosomal origin. These data represent the first direct evidence of tick miRNA-mediated regulation of vertebrate host gene expression at the tick-host interface (Hackenberg M et al., 2017, RNA. 23, 1259–1269), providing candidate miRNAs for drug discovery efforts.
Tripartite interactions between the disease vector/vector-borne pathogens and the host
Noncoding RNAs (ncRNAs) are now known to be (I) transmitted by the vector to possibly modulate vertebrate host responses and (II) regulated in the host by parasites to favor parasite survival. We provided an overview of the involvement of ncRNAs in the parasite-vector-host triad and their effect on host homeostasis (Bensaoud et al., 2019, Trends Parasitol. 35, 715–724). We also reviewed the role that nanovesicles play during pathogen spread, host colonization, and disease pathogenesis (Chávez et al., 2019, J Cell Sci. 132, jcs224212), focusing on a potential role for arthropod exosomes in this tripartite interaction, especially as carriers of long non-coding (lnc)RNAs (Hackenberg and Kotsyfakis, 2018, Trends Parasitol. 34, 549-552).
Towards application development
Two primary interests have driven research into tick salivary secretions: the search for suitable pathogen transmission blocking or "anti-tick" vaccine candidates and the search for novel therapeutics derived from tick salivary components (Chmelař et al., 2019, Front Physiol. 10, 812). We reviewed the major tick salivary protein families exploitable in medical applications (Chmelař et al., 2019, Front Physiol. 10, 812).
Diverge or converge: do harsh abiotic condition restrict divergence of defences in alpine willows?
Plants employ a bewildering diversity of defences to withstand herbivory pressure and detrimental environmental conditions. Exploring the factors that drive the variability in plant defensive strategies is crucial for understanding plant evolution in face of herbivory and harsh environment. Within this project we aim at addressing the question: How the interplay between herbivory and environmental pressures form the evolution of plant chemical defences? To achieve this, we combine state of the art metabolomics and bioinformatics combined with field sampling of highland and lowland species of willows. The core of the project includes analysing macroevolutionary patterns in willow defences and comparing them between highland and lowland species. This project will show that changes along elevational gradients strongly affect the way how host-plant defences evolve, directing the prevalent macroevolutionary trends among related willow species (Figure 2).
Figure 2. Proposed elevational trends in plant defences. Higher biomass costs at high elevations drive an increase in plant defences and support defensive stragies and evolutionary trends alternative to the ones shown by lowland plants.
Supra-specific Janzen-Connell effects: Constraints to insect herbivore specificity and performance
Plants possess complex suites of evolved defensive traits which serve to determine their palatability for insect herbivores (Fig. 3), and in turn the specificity of insects feeding on them. From the evolutionary perspective, the need to avoid sharing specialized herbivores should promote divergence in defensive strategies among closely related hosts, such as the investment into constitutive vs. induced defenses. This may increase the potential for an insect specificity and performance gradient across congeneric hosts, potentially affecting negative density dependence effects among closely related plants. Within this collaborative project, we take two complementary approaches to manipulate the chemical landscape faced by insect herbivores. Our first objective is to examine whether highly specific induced defenses promote evolutionary divergence in defensive strategies in large tree genera (Ficus, Syzygium, and Macaranga), and hence lower negative density dependence effects in the spatial distribution of species with divergent defenses. Our second objective is to relocate the insects themselves across increasing phylogenetic and chemical distances from their primary hosts.
Fig. 3. A. Variation in caterpillar communities explained by Ficus, Macaranga, and Syzygium polyphenol profiles, B: Food-web between focal plants and caterpillars.
Multi-taxa responses of tropical Lepidoptera to climate changes and anomalies on Barro Colorado Island in Panama
Climate changes represent one of the major causes of global biodiversity decline with species attrition and plausible dramatic scenarios for terrestrial biodiversity concentrated in the tropics. Extreme droughts and disruption in rainfall have been affecting species composition and productivity among multiple organisms. However, we still have little understanding of the effects of climate changes on terrestrial organisms responsible for the maintenance of crucial ecosystem services, such as insect herbivores. Our main objective seeks to understand the multiple responses of tropical Lepidoptera to ongoing and predicted climate changes. We predict contrasting changes in ten phylogenetically and ecologically Lepidoptera taxa and study their past and future directional responses to extreme events of climate that occurred during 2009-2020. We will compare species responses using three different analytical approaches and models to explore the best choice of target model species for monitoring programs and studies of climate change. Our study system also includes reproducible field protocols, laboratory experiments (thermal and desiccation tolerance) and data modelling.
Duration: 01-01-2019 to 01.06.2022
Integrating genomic and trophic information into long-term monitoring of tropical insects: pollinators on Barro Colorado Island, Panama
Current evidence suggests insect pollinators to be undergoing population declines worldwide with catastrophic consequences to biodiversity and human crop production. These population declines are difficult to demonstrate using census data alone. High-throughput sequencing techniques such as RAD-seq allow to generate single nucleotide polymorphism datasets, permitting the estimation of population genetic parameters such as effective population size. Using collections from long-term monitoring efforts allow to study how populations have been recently affected by factors such as climatic change. We will analyze recent population changes of diverse insect pollinators (euglossine bees, Cyclocephalini beetles and butterflies). The ForestGEO Arthropod Initiative has been monitoring arthropod assemblages on Barro Colorado Island, Panama, since 2009. We will use these data to infer population genomic changes in the 25 most common pollinator species. We will improve forecast of population dynamics using flower resource, determined from DNA pollen metabarcoding and litterfall trap data, as covariates of pollinator time-series. In sum, we will study recent population changes of insect pollinators in a tropical rainforest. We will develop models of population dynamics for the 25 most common species, incorporating genomic and trophic information.
Duration: 01-01-2020 to 01.01.2023
Connections between maintenance of diversity and variation in nature
How do species coexist in diverse ecological networks despite competition, predation and parasitism? This is the most enigmatic question in community ecology, with an analogy at the population level: How is genetic variation maintained within species despite selection and drift? These twin questions are typically studied separately, yet diversity and variation are likely interdependent, with important consequences for basic understanding and biodiversity conservation.
ERC-CZ grant (2020 - 2025)
Network structure and function
We study how the structure of ecological networks relates to their function - stability and resilience to climate change and biological invasions. Large proportion of research into ecological networks relies on assumption that structure of the networks is decisive factor for their function and resilience, but there are very few direct experimental tests of this question. We are performing these experimental tests and study how temperature and timing of interactions impact the outcome of species interactions and network dynamics.
CSF grants (2017 - 2019, 2020 - 2021)
Innovation of integrated potato protection against the Colorado potato beetle based on new knowledge of genetic and biological characteristics
Colorado potato beetle (CPB) is our main pest in the above-ground mass of potatoes with the potential for crop losses up to 50%. However, protection against it is currently very difficult due to insecticide resistance. In addition to the use of chemical protection and controversial genetic modifications, the development and use of biological protective methods are becoming increasingly promising. Use of entomopathogenic fungi (EPF) and parasitic nematodes (EPN) for protection does not cause a pest resistance. A great advantage is the support in use of mycoinsecticides by sustainable and organic farming programs. Apart from conservation studies, molecular and genetics methods are used wordwide to address the invasive and genetic potential of CPB. Project NAZV ZEMĚ 3 č. QK1910270; PI: Oxana Skoková Habuštová.
Fungicidal and insecticidal additive for plant growing substrate
The subject of this project is to verify the concept of a biological additive to a plant growing substrate based on a combination of a mycoparasitic fungus, an entomopathogenic fungus and an entomopathogenic nematode (“3 in 1 preparation”). The aim of this sub-project will be to select a suitable species and strain of mycoparasitic fungus that will effectively suppress plant pathogens and will be compatible with these entomopathogenic organisms. The aim of the project will be to design and verify the technology of additive production, storage conditions and verify its effects in laboratory and greenhouse experiments on model types of plant diseases and pests. It will include the development of in-vitro nematode cultivation technology, which should significantly reduce the cost of production compared to existing technology using insect hosts. The result should be a preparation which, in addition to pests, will also suppress, for example, the causative agent of a disease called the fall of seedlings (Pythium spp., Fusarium spp., Rhizoctonia spp.). Technology Agency of the Czech Republic project No. TG02010034; PI: R. Zemek.
Protective measures against the double spined bark beetle, Ips duplicatus
The aim of the project is to fill in gaps in the knowledge of biology and propose effective methods of management of a new pest of spruce monocultures in the Czech Republic, the double spined bark beetle. Field experiments will verify the effectiveness of new protective measures such as standing poisoned trap trees prepared by surface spraying and/or microinjection of insecticides as well as their impact on non-target arthropod species. Due to the unknown abundance of the double spined bark beetle, it is necessary to clarify the actual proportion of timber infested by this pest. Without such knowledge no precise calculation of the number of protective measures can be made. Project TAČR ZÉTA No. TJ02000025; PI: Markéta Davídková.
Novel methods of treatment of harvested wood infested with bark beetles
Current methods of treatment of harvested wood infested with bark beetles are largely based on insecticidal spraying. The aim of the project is to verify the effectiveness of novel biological and environmentally friendly methods based on specific inhibition of digestive enzymes of bark beetles, application of entomopathogenic nematodes and some other bioinsecticides (e.g. azadirachtin). Project supported by Grant Agency of the Forests of the Czech Republic, state enterprises, 11/2017; PI: Petr Doležal.
Selected aspects of bionomy of the large pine weevil and their importance in forest protection
The large pine weevil is a significant pest of coniferous plantations in the Czech Republic. Adults live up to five years, while life expectancy, fertility and rate of development depend on the species of host tree in which adults developed. The aim of the project is to provide the above-mentioned characteristics for the most important domestic species of conifers, as well as gain information on the mechanisms of overwintering and cold resistance of larvae and adults. Special attention will be given to the effectiveness of various mechanical methods of seedling protection available on the market. Based on the results, protective measures against this pest and the species composition of seedlings planted on clearcuts will be adjusted. Project supported by Grant Agency of the Forests of the Czech Republic, state enterprises, 08/2017; PI: Petr Doležal.
Bionomy of cambioxylophagous insects on Scots pines in the Czech Republic – unknown aspects and practical importance
High temperatures and lack of precipitation in recent years resulted in local outbreaks of insect pests of pines at numerous localities in the Czech Republic. The aim of the project is to obtain information on the composition of the cambioxylophagous fauna of Scots pine at selected localities in central Bohemia, Vysočina region and south Moravia. For the most important species, basic knowledge about their bionomy will be obtained. Field tests of the efficiency of protective measures based on commercially available pheromone dispensers as well as trap trees will be performed. Based on the results, suitable management options shall be proposed. Project supported by Grant Agency of the Forests of the Czech Republic, state enterprises, 00002-2019-99-48; PI: Petr Doležal.
Endocrine control of stress situations
The goal of the project is to better understand the physiological and biochemical processes that insects' bodies go through in response to stress. These processes are triggered by peptides from the adipokinetic hormone (AKH) family. The study focuses on the function of AKH in the defence response to pathogens like entomopathogenic nematodes and fungi, as well as against naturally occurring toxins like the venom of the honey bee Apis mellifera and the parasitic wasp Habrobracon hebetor. Additionally, the project involves examining the mechanisms by which AKHs encourage pathogens to intensify their negative effects on the host organism. The emphasis is placed (1) on the study of anti-oxidative stress reactions, including their biochemical mechanism of action, (2) on the analysis of ultrastructural changes in insect tissues (muscles) after the application of toxins, and (3) on the function of enzymes, nutrients, and other metabolites in stressful situations that disrupt the insect organism's homeostasis.
PI: Dalibor Kodrík
Evolution of parasitism in apicomplexan parasites (Sporozoa; Apicomplexa)
We are getting more interested in the evolution of parasitism in Apicomplexa. We recently published a novel hypothesis about the evolution of obligate parasitism in Apicomplexa from the photoparasitic ancestor (Oborník 2020). We suppose that the phototrophic ancestor of apicomplexan parasites had already combined phototrophy and parasitism, as the chromerid alga Chromera velia likely does. It appeared that C. velia invades coral larvae and causes the death of a substantial portion of the larval population. The photoparasitic lifestyle of the chromerid is allowed by the translucency of the larvae making thus photosynthesis possible. We suppose the photoparasite acquires nitrogen preferably from the host because it can fix the organic carbon by its own photosynthesis.
Mutualistic dynamics
Many mutualisms rely on inter-specific resource-service exchanges (e.g., pollination, ant fungus gardens, cleaning mutualisms). Our goal is to study how resource-based mutualisms embed within food webs, and their effects on the dynamics and diversity of ecological communities. This is accomplished by modelling of the dynamics of resource production (e.g., nectar, pollen, honeydew) and the effects of their consumption on the dynamics of producers and consumers (the mutualists), as well as third parties (e.g., competitors, herbivores, predators). Adaptability (e.g., by behavior or evolution) in the provision of resources and services is also considered. This research can advance our understanding natural communities, and the consequences of species invasions and management.
Nematode diversity and phylogeny
Within this long-term project, we focus on studying diversity and phylogeny of entomopathogenic and molluscoparasitic nematodes and their bacterial associates. Our studies in EPN and MPN systematics in the last years significantly contributed to our understanding of their diversity by discovering of 5 novel EPN species, and 5 MPN species, with important redescription of Alloionema appendiculatum. We found that the most important genetic marker in EPN systematics, the Internal Transcribed Spacer (ITS) displays larger variability within nematode individuals than between some established steinernematid species. Our results thus significantly affected the systematics and phylogenetic reconstructions of steinernematid EPN. Recently, we documented co-cladogenesis of bacterial symbiont Xenorhabdus indica and its steinernematid nematode hosts (Nermuť et al., 2015; Půža et al., 2015; Bhat et al. 2019).
Applications
Within this long-term project we study primarily the possibilities of the use of entomopathogenic and molluscoparasitic nematodes in biocontrol. Recently, we assessed the possibility of the use of entomopathogenic nematodes for the control of the bulb mite Rhizoglyphus robinii. This study has shown that EPNs can invade and kill bulb mite but the mortality is not sufficient for the use of EPNs against these pests. In similar way and with similar results we investigated whether the slug parasitic nematode Alloionema appendiculatum could be used in the control of noxious slugs Arion spp. Presently we investigate the possibility of EPN use against Colorado potato beetle and bark beetles. Within this project we also identified the method of DNA extraction for taxonomic identification of early developmental stages of forensically important flies (Calliphoridae and Sarcophagidae). It was adopted for the routine work at the Department of forensics of the Institute of Criminalistics, Prague. Important publications: Nermuť et al, 2019a; Nermuť et al. 2019b; Olekšáková et al., 2018.
Interactions
We are strongly interested in various interactions between parasitic nematodes and other organisms. For this reasonwerecently collaborated on the development of the real-time qPCR method that enables tracing entomopathogenic nematode (EPN) ecology, distribution and interactions with other organisms. We showed that competition for insect cadavers exists between entomopathogenic and free-living nematodes and that some facultatively parasitic nematodes act as facultative kleptoparasites which can readily explain the low EPN numbers in field samples.Also a qPCR-based method was developed for the detection of molluscoparasitic nematodes (MPN) in soil and host tissues. The method represents a new tool to unravel the ecology of nematode-slug complexes. More recently, we focused on the interaction of EPNs and entomopathogenic fungi (EPF) where we revealed that EPNs may act as vectors for EPF andenhance the efficiency of fungal dispersal. Important publications: Campos-Herrera et al., 2015; Campos-Herrera et al., 2016; Jafffuel et al., 2019; Nermuť et al. 2020.
Impact of combined stressors on freshwater biota
We aim to unravel the combined impacts of anthropogenic chemical pollution and climate change on freshwater ecosystems, using a combination of laboratory and mesocosm experiments focusing on the biota of small standing waters dominated by freshwater invertebrates. We currently lack data and unified framework to predict responses of freshwater ecosystems to these combined stressors. To fill this knowledge gap, we will use laboratory and mesocosm experiments to understand how commonly found pharmaceutically active compounds (PhACs) and pesticides in combination with warming affect individuals, trophic interactions, whole ecosystems and energy flow in communities in small standing waters.
Research team: D. Boukal (PI), V. Kolář, A. Csercsa
External collaborators: C. Duchet (Faculty of Science, University of South Bohemia), T. Randák, K. Grabicová (both Faculty of Fisheries and Protection of Waters, University of South Bohemia), R. Stoks (KU Leuven)
Communities of freshwater insects and other invertebrates in human-impacted standing waters
We compare freshwater communities in fly ash lagoons, nearby sandpit ponds and fishponds to describe the biodiversity and conservation potential of man-made sites. We study both conservation value and ecology of communities of these sites using a combination of a landscape-scale field survey with laboratory experiments, field enclosure experiments, and analyses of heavy metal content across trophic levels and taxa. This multi-level approach will provide evidence-based recommendations for the restoration and management of man-made habitats including fishponds, and contribute to the broad understanding of their biodiversity.
Research team: D. Boukal (PI), V. Kolář, B. Carreira
External collaborators: R. Tropek, A. Landeira-Dabarca (Institute of Entomology), L. Vebrová, M. Poláková, O. Skácelová-Lepšová (Faculty of Science, University of South Bohemia), R. Stoks (KU Leuven)
Freshwater ectotherms under climate change: the role of phenotypic plasticity in life histories and trophic interactions
Understanding climate change impacts on ecosystems is one of the most important challenges to current ecology and conservation biology. While many freshwater ectotherms are particularly vulnerable to rising temperatures due to their limited dispersal ability, they may mitigate the impact of thermal stress by plastic responses. However, the role of phenotypic plasticity in the context of climate change is little understood. Using laboratory experiments and numerical simulations, we examine the role of individual thermal performance curves and thermally induced plasticity in life histories and species interactions of freshwater ectotherms under the anticipated climate change.
Research team: D. Boukal (PI), A. Csercsa, S. Dijoux
External collaborators: J. Mocq, J. Okrouhlík (Faculty of Science, University of South Bohemia), L. Gvoždík (Institute of Vertebrate Biology CAS), A. Sentis (University of Aix-Marseille)
Biogeography and speciation of New Caledonian mayflies (Ephemeroptera)
New Caledonia, a Melanesian archipelago with extraordinary diversity and endemism, is considered a global-scale biodiversity hotspot. The most intensively studied biological phenomenon in New Caledonia is the origin of its biota in relation to its geological history, involving the separation from Gondwana, accretion of terranes, and marine submersion. In our project, we focus on the processes shaping the biodiversity of aquatic ecosystems of New Caledonia based on mayflies (Ephemeroptera). The local fauna includes a single family (Leptophlebiidae) with a broad spectrum of ecological adaptations analogous to the Darwin’s finches in the Galapagos. Our research aims to chart the diversity of New Caledonian mayflies and unravel their origin and evolutionary history.
Research team: Ľ. Hrivniak (PI), P. Sroka, R. Godunko
External collaborators: J. Bojková (Masaryk University, Brno), M. Sartori a J-L. Gattolliat (Cantonal Museum of Zoology, Lausanne)
Larval specializations, bionomics, and habitat shifts in two selected orders of Insecta during the Mesozoic
Ontogenetic diet and habitat shifts from larvae to adults allow them to efficiently explore resources and minimize intraspecific competition. This evolutionary advantage helped insects become the most speciose group of organisms on Earth. However, larval adaptation of fossil insects are insufficiently explored. We will focus on new material of Mesozoic insects. This crucial period for insect evolution was characterized by accelerated diversification in some lineages connected with profound changes in the palaeoclimate and palaeoecosystems. As model taxa, we will use aquatic Ephemeroptera and terrestrial polyphagan Coleoptera that cover a wide range of newly established palaeohabitats. This approach will allow us to track habitat shifts and stases in their evolutionary history.
Research team: P. Sroka, R. Godunko
External collaborators: J. Prokop (PI), J. Batelka, K. Rosová (Charles University, Prague), A.H. Staniczek (Stuttgart State Museum of Natural History)
Mayflies of the Caucasus Mts
Freshwaters of the Caucasus Mountains host exceptionally high biodiversity and endemism. Mayflies (Ephemeroptera) constitute an important component of this unique fauna. We undertook many fieldtrips to the area during the past decade and collected an extensive material, that is still being processed. Our aim is to provide a complex information on the diversity, identification, and distribution of Caucasian mayflies, which will enable to better use their potential in hydrobiology, water quality assessment, and conservation. We will also examine the origins and mechanisms driving diversification of the local mayfly fauna to understand the evolutionary history and formation of endemism in relation to the geological history of the area.
Research team: R. Godunko, Ľ. Hrivniak, P. Sroka
External collaborators: J. Bojková (Masaryk University, Brno), A.V. Martynov (National Museum of Natural History, Kiev), D.M. Palatov (Moscow State University)
Biogeography and diversification of Neotropical biodiversity
The American tropics, or the Neotropics, is a biogeographic region home of unique animal and plant species. The rich diversity of life, forms, and genes found in this region goes hand in hand with the variety of climate, landscapes, and elevations. A long-standing question, since the time of early naturalists, is still unresolved: is the unique and rich biodiversity of the Neotropics the result of environmental complexity?
We use phylogenomic datasets to infer robust species trees, which are critical to resolve evolutionary relations, estimate divergence times, and study the tempo and mode of species diversification. Furthermore, the phylogenomic trees provide information on how regions become sources or sinks of diversity by means of dispersal.
Phenotypic evolution and convergence in Neotropical butterflies
Butterfly wing morphology and colors are under strong selective pressure by mates and natural enemies. Rates of phenotypic evolution can be decoupled from molecular and diversification rates, resulting in distantly related species resembling each other or closely related species having disparate morphologies.
Mimicry in butterflies is a classic example of natural selection, where predators associate an unprofitable prey with warning colorations. The Neotropics harbors several mimicry rings of unrelated butterfly species resembling each other. We study the convergent evolution of skipper butterflies in the subtribe Eudamina (Hesperiidae) by quantifying phenotypic rates (wing shapes and colors) in a phylogenetic framework. Furthermore, we carry out behavioral experiments in the lab to test theoretical predictions of mimicry using models of Neotropical butterflies.
Ecological and population genomics
Species and their genomes are under constant interaction with the environment. The responses of genomes, at local and regional scales, can be quantified using efficient tools such as high-throughput DNA sequencing. We aim to understand how past changes in the landscape and climates have shaped the diversity and distribution of populations.
We study local adaptation and signatures of selection in the genomes of butterflies. We estimate how the Pleistocene climatic fluctuations have modulated the structure and gene flow of populations across geographic regions. We also study genomic islands of divergence among sympatric species with high morphological resemblance that are either closely related (sister species) or evolutionarily distant.
Role of telomerase in eusocial insects
Using the cockroach Periplaneta americana (a representative of solitary hemimetabolous insects) and workers of honeybees (Apis mellifera, a representative of eusocial holometabolous insects), we showed that development and aging in insects associate with a decline of telomerase activity (Chromosome Research (2014) 22:455-503; Korandova and Frydrychová (2016) Chromosoma 125: 405-411). Nevertheless, telomerase activity in the somatic tissues of honeybee queens and reproductive individuals in termites is strongly upregulated compared to that in workers or soldiers of the same species. It suggests that upregulation of telomerase activity may be linked to the caste differentiation process and lifespan extension of kings and queens in eusocial insects (Korandova and Frydrychová (2016); in press).
Bombus terrestris (Hymenoptera: Bombini) is a hymenopteran species with primitive social organization and, compared to advanced social insects such as A. mellifera, have several distinct features. For instance, colonies of B. terrestris are annual and have smaller population sizes than those of more advanced social insects. After a relatively long diapause, their queens undergo both solitary and social phases. In general, bumblebee queens are only slightly morphologically different from workers. We studied telomerase activity in B. terrestris to see if this species, despite its primitive social organization, has the same pattern in telomerase activity as observed in A. mellifera. Among tested somatic tissues of B. terrestris, telomerase activity was found only in the fat bodies of young pre-diapause queens and associated with increased DNA synthesis (Figure 1). We speculate that the upregulation of telomerase activity and DNA synthesis in the queens are essential for rapid intensification of metabolic activity in the fat body to build up a sufficient energy reserve prior to diapause. Our data support the hypothesis that the lifespan differences between B. terrestris workers and queens are simply related to the long diapause period. We propose that there are differences in lifespan regulation between primitive and eusocial insect species (Koubová et al. (2019) IBMB 115:103241).
Currently, the role of telomerase in eusocial insects is investigated in more detail.
Seasonal effects on telomerase activity and aging in honeybees
In honeybees, the rate of aging is modulated through social interactions and seasonal effects. Winter generation workers, which hatch at the end of summer, have remarkably extended lifespans as an adaptation to the cold season when the resources required for the growth and reproduction of colonies are limited and the bees need to maintain the colony until the next spring. In contrast, the summer bees only live for several weeks. To better understand the lifespan differences between summer and winter bees, we studied the fat bodies of honeybee workers and identified several parameters that fluctuate in a season-dependent manner. We reported that telomerase activity, DNA replication, fat body mass, and vitellogenin levels gradually increased as the winter season proceeded (Figure 2). Our study showed that although the fat bodies of winter bees differ significantly from those of summer bees, these differences are not a priori set when bees hatch at the end of summer or in early autumn but instead gradually evolve throughout the season, depending on environmental factors (Koubová et al. (2021) Scientific Reports 11:1-11).
Currently, we investigate effects of various environmental factors on honeybee aging in more detail.
Plant-insect food webs in tropical rainforests
This study examines extremely complex plant-insect food webs in tropical forests, particularly in Papua New Guinea, and ecological and phylogenetic determinants of their structure. In particular, we examine species richness and host specificity of herbivorous insects from multiple guilds on plant species selected across entire plant phylogeny. Further, we study associated parasitoids and predators, particularly ants, spiders and also birds. Our analytical approaches include the study of plant phylogenetic relationships and their signal in insect trophic interactions, as well as manipulative experiments investigating the importance of predators on herbivores and, by extension, on plants. Key publications: Novotny et al. (2002, Nature 416: 841-4), Weiblen et al. (2006, Ecology 87: S62-75), Novotny et al. (2010, J. Anim. Ecol. in press).
Mapping of Butterflies of the Czech Republic
Butterfly fauna of the Czech Republic consists of 161 species. As many as 18 have already been lost, and about half is endangered. See lepidoptera.cz for National recording scheme, coordinated by our member Jiri Benes.
Biodiversity and restoration of postindustrial sites
In the impoverished European landscapes, stone quarries, open mines, spoil heaps, sandpits, or fly ash deposits serve as crucial secondary refuges for various species of threatend habitats, such as steppe grasslands, bare sands, and open forests. Very often such post-industrial sites serve harbor many endangered oranisms vanishing from our common landscapes. Recently, we have revealed fly ash deposits as one of the most important habitats for conservation of Central European biodiversity. We have also repeatedly shown that commonly practiced technical reclamations cause local extinctions of majority of such species and thus waste this tremendous conservation potential. We study also effects of various environmental factors on forming of insect communities and their utilisation during the effcient ecological restoration. Currently, we focus mainly on various finely-grained substrates, including fly ashes, and surprisingly overlooked post-industrial freshwater habitats.
Key publications: Tropek et al. 2010 Journal of Applied Ecology; Tropek et al. 2013 Biol. Conserv.; Tichanek & Tropek 2015 J. Insect Conserv.
English book with our contributions: Řehounková a kol. 2011. Near-natural restoration vs. technical reclamation of mining sites in the Czech republic.Calla, České Budějovice. (http://www.postindustrial.eu/en/knihy)
Forest management and restoration
We focus on conservation of woodland associated insects and their biodiversity, predominantly in temperate forests of low or middle elevations. We explore how different forest managements affect diversity and composition of insect communities, mainly those of saproxylic beetles, but also butterflies, moths, bees and wasps or other groups. We are particularly interested in the management of protected woodland areas where biodiversity conservation is the primary objective. In this context, we often show that traditional silvicultural practices, such as coppicing, wood-pasture or pollarding, may serve as useful tools in conservation and ecological restoration of temperate woodlands.
Related publications:
Weiss et al. 2021: The effect of coppicing on insect biodiversity. Small-scale mosaics of successional stages drive community turnover. Forest Ecology and Management.
Thorn et al. 2020: Estimating retention benchmarks for salvage logging to protect biodiversity. Nature Communications.
under construction: the linden bug:
Pyrrhocoris apterus as a new model species
The linden, Pyrrhocoris apterus, served as an excellent model of classical insect endocrinology for more than 50 years. However, neither functional genetics, nor genomic tools were available. Our goal is to introduce these techniques to P. apterus and establish this insect species as a model organism with full palette of experimental tools, especially:
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Reverse genetics: Systemic RNA interference is routinely used for gene knock down in P. apterus (see Smykal et al. 2020, Bajgar et al., 2013a; Smykal et al., 2014; Buresova et al., 2016). To create either complete null mutants or specifically modify gene of interest, we established genome editing in P. apterus (Kotwica-Rolinska et al. 2019). Or first unique mutants are phenotypically characterized.
- Neuropeptide inventory: P. apterus served as a model for insect endocrinology, yet, its neuropeptide repertoire is only very poorly known. Therefore we prospected the genome and transcriptome for genes and transcripts coding for neuropeptides and their receptors. The physical existence of processed peptides is further confirmed by MALDI-TOF-MS/MS in collaboration with Dr. Christian Wegener (Wurzburg University), and anatomical localization is assessed with ICC experiments. See Aska's paper on a new insect neuropeptide (Kotwica-Rolinska et al.).
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Microsurgery: The size and anatomy of P. apterus allows for fine microsurgical operations, such as removing Corpus Allatum (P. apterus has only one gland), extirpation of pars intercerebralis region (Bajgar et al., 2013b), or eye removal.
Neutralizing nanobodies as potential therapeutics for tick-borne encephalitis
(Czech Health Research Council, 2022-2025, Co-PI Martin Palus)
Pathogesis and therapy of emerging viral diseases
(The National Institute for Virology nad Bacteriology, 2022-2025, coordinator for BC: Daniel Růžek)
Coevolution between Galápagos mockingbirds and their ectoparasites
Galapagos mockingbirds comprise four species of recently radiated passerines endemic to the Galapagos archipelago. Co-analysing mitochondrial and nuclear markers of mockingbirds and their ectoparasites the most likely scenario of colonisation of particular islands within the archipelago was reconstructed. Link between population size, geographical range and parasite load is being analysed using high-throughput sequencing of MHC genes and neutral multilocus markers. Obtaining knowledge of MHC gene diversity is also of conservation interest, since several species of mockingbirds are threatened or even extinct in their original area of distribution (e.g. Floreana mockingbird). (P.I.: J. Štefka)
MYXOZOA
Myxozoans are diverse group of cnidarian parasites, that have been morphologically highly reduced as an adaptation to parasitism and that have conquered a range of different aquatic habitats. Myxozoans have a complex life cycle involving a vertebrate (fish) and an invertebrate (bryozoan, polychaete or oligochaete) host and some species cause important losses in the aquaculture sector. We conduct a wide range of studies on myxozoans:
Pyroseq: Pyrogenic organic matter sequestration in forest soils affected by climate change
Czech Science Foundation (CSF), principal investigator, 2024-2026
Forest wildfires lead to the production of chemically altered biomass residues known as pyrogenic organic matter (pyOM), which has been thought to be highly resistant and contribute to soil organic carbon (SOC) sequestration. A significant portion of pyOM may, however, be utilized by soil biota and as such may be fragmented, digested, and released as carbon dioxide into the atmosphere or stabilized in the soil. In addition, soil succession after the fire event and climate change may have a significant effect on all of the biotic processes. Here, we observe successional changes in the soil properties on a 100-year post-fire chronosequence in pine forests in the Mediterranean, temperate, and boreal zones and along the soil profile. The focus is on the effect of increased temperature on the transformation and stabilization of pyOM by soil faunal and microbial communities. The proposed project consists of field samplings and observations, 13C-labelled pine litter and pyOM production, as well as a slightly manipulated field experiment and a heavily manipulated laboratory experiment.
Fungicidal and Insecticidal Additive for Plant Growing Substrate
The subject of this project is to verify the concept of a biological additive to a plant growing substrate based on a combination of a mycoparasitic fungus, an entomopathogenic fungus and an entomopathogenic nematode (“3 in 1 preparation”). The aim of this sub-project will be to select a suitable species and strain of mycoparasitic fungus that will effectively suppress plant pathogens and will be compatible with these entomopathogenic organisms. The aim of the project will be to design and verify the technology of additive production, storage conditions and verify its effects in laboratory and greenhouse experiments on model types of plant diseases and pests. It will include the development of in-vitro nematode cultivation technology, which should significantly reduce the cost of production compared to existing technology using insect hosts. The result should be a preparation which, in addition to pests, will also suppress, for example, the causative agent of a disease called the fall of seedlings (Pythium spp., Fusarium spp., Rhizoctonia spp.).
Funding: Technology Agency of the Czech Republic; Project No. TP01010022 (PI: R. Zemek).
Key outputs:
Konopická J., Zemek R., Tan J., Palevsky E. (2024) Kmen houby Trichoderma harzianum CCM 9213 a použití tohoto kmene v přípravku pro podporu růstu rostlin a pro ochranu rostlin proti houbovým patogenům Patent č. 310080. Úrad pro průmyslové vlastnictví, číslo patentového spisu: PV 2023-28
Zemek R., Nermuť J., Konopická J., Bohatá A. (2022) Insekticídne a akaricídne aditívum do nosného substrátu na pestovanie rastlín Patent č. 288968. Úrad priemyselného vlastníctva Slovenskej republiky.
Functional Genomics of ticks
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RNA interference (RNAi): This well-established technique allows us to silence specific transcripts in ticks, revealing the critical roles their protein products in their biology.
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Ex vivo membrane feeding with protein inhibitors: This method enables us to deliver enzyme inhibitors and receptor blockers to ticks while they feed, providing insights into the functions of specific proteins and pathways within the context of blood feeding.
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Laboratory models for tick-borne diseases: We have set up in our laboratory, complete transmission models for Borrelia, Babesia, and Anaplasma infections. We use them mainly to test the involvement of tick candidate genes in tick-pathogen interactions using the RNAi method.
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Tick innate immunity: We explore how ticks defend themselves against pathogens and other threats.
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Haemoglobin and iron biology: We unravel the intricate processes by which ticks manage ingested blood components like haem or iron from host blood macromolecules.
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Proteolytic systems and protease inhibitors of ticks: We examine the enzymes involved in breaking down blood proteins in the tick's digestive system and enzymes or inhibitors secreted by the salivary glands to facilitate feeding.
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Chitin biology: We study chitin, a key component of the tick's exoskeleton, and its role in tick development and molting and transmission of pathogens.
PMID: 34450130
Heme: a putative master regulator in trypanosomatids
Heme is one of the most important cofactor in extant organisms, constituting a reactive core of many diverse hemoproteins. Unlike most eukaryotes, trypanosomes and leishmanias are not able to synthesize heme and thus belong to heme auxothrophs. In order to shed light on how they utilize heme acquired from their hosts, we aim to dissect the function of heme transporters in model human parasitesTrypanosoma brucei and Leishmania mexicana. Moreover, we hypothesize that heme may be the key factor driving metabolic changes throughout the life cycle of both pathogens, with important difference between the stages from insect vector and mammalian blood. One of the most common heme-containing enzymes is catalase detoxifying cell from H2O2. Surprisingly, catalase is present only in monoxenous (= insect-only) flagellates but absent from all their dixenous (insect + mammalian hosts) relatives. Our preliminary data show that when overexpressed in dixenous T.brucei and L.mexicana, catalase is active only in the insect stages and loses its activity in the vertebrate-parasitizing stages. We want to analyze inter-stagial differences in heme acquisition in trypanosomatids and the reasons and mechanism behind the intriguing multiple losses of catalase in blood-dwelling parasites.
Queuosine: The role of an essential tRNA modification in parasitic protist Trypanosoma brucei
Transfer RNAs are typical for the large number of posttranscriptional modifications. Most of the tRNA modifications are present in the anticodon loop, which have crucial role in proper translation of proteins. Queuosine is one of the most complex tRNA modifications. Despite its omnipresence among bacteria and eukaryotes, role of queuosine tRNA modification is not clear. The main aim of this project is to evaluate the function and subunit composition of the enzyme responsible for queuosine formation in T. brucei. Using the RNAi knock-down strategy we want to address the principal question regarding the role of queuosine tRNA modification with respect to biology and physiology of this protozoan parasite.
Antigeny pro novou vakcínu proti klíšťatům a jimi přenášeným patogenům
GAČR 13-27630P (2013-2015)
Klíšťata jsou krevsající parazité a vektoři závažných virových, bakteriálních a protozoálních onemocnění lidí a zvířat. Ixodes ricinus je klíště běžné v České republice a Evropě, kde přenáší klíšťovou encefalitidu (TBE), Lymeskou boreliózu, anaplazmózu nebo babeziózu. Imunizace hostitelů rekombinantními klíštěcími proteiny postihuje sání klíšťat a brání přenosu patogenů z klíštěte na hostitele. Nicméně, dostupné klíštěcí antigeny stále nejsou dostatečně účinné. Zde navrhujeme pomocí metody RNA interference (RNAi) otestovat geny klíštěcí dráhy metabolismu železa a hemu za účelem nalezení vhodných vakcinačních kandidátů postihujících sání a vývoj klíšťat. Tito kandidáti budou rovněž testováni na svůj potenciál bránit přenosu borélií z klíštěte na hostitele. Věříme, že vakcinace hostitelů těmito proteiny má velký potenciál jako strategie vedoucí k redukci počtu klíšťat a přenosu patogenů.
MitoSignal: Determining signaling mechanisms that drive cellular differentiation of Trypanosoma brucei
Mitochondria perform three essential functions: ATP production, metabolite synthesis and cellular signaling. These signals, communicating the bioenergetic and biosynthetic fitness of the organelle to the nucleus, play a powerful role in determining cellular fate.
Our lab focuses on incorporation of mitochondrial reactive oxygen species (mROS) in cellular signaling. We utilize the unicellular parasites, Trypanosoma brucei and T. congolense, as simplified but elegant models to define mROS-driven cellular differentiation. As these protists undergo programmed development between several distinct life cycle forms, there are striking changes to the structure and physiology of their single mitochondrion that manifest in elevated ROS levels. Importantly, we demonstrated that these ROS molecules are essential for the developmental progression of the parasite. Employing these well-chosen models and combining next-generation biosensors, advanced bioenergetic methods, redox proteomics and a CRISPR/Cas9 genetic screen, we are answering the following fundamental questions: Does mROS drive Trypanosoma cellular differentiation? What molecular processes are responsible for the elevated mROS levels during differentiation? How is the redox signal propagated to the rest of the cell? Our research aspires to unravel the fundamental mechanisms underlying the intricate communication between mitochondria and the rest of the cell, featuring cellular hallmarks of cell fate decision.
Molecular epidemiology of cryptosporidiosis
Cryptosporidium andersoni and C. muris are two known species of gastric cryptosporidia recorded from mammals. The infectivity and pathogenity of C. andersoni in neonatal calves and both gastric Cryptosporidium species in Mongolian gerbils (Meriones unguiculatus) were molecularly and histologically characterized. Mastomys coucha was described as a new host susceptible to C. andersoni. Neonatal animals were more susceptible to infection with gastric cryptosporidia. The changes of viability and infectivity of gastric and intestinal cryptosporidia are studied in long-term experiments.
Pig cryptosporidiosis has been described in all age categories. Cryptosporidium suis and Cryptosporidium pig genotype II were dominant species in pigs. Very low occurrence of C. parvum in pigs has been recorded but C. parvum and C. andersoni were dominant species infecting cattle younger than two months of age and adult animals, respectively. Cryptosporidium bovis was found with very low prevalence and C. ryanae was not detected. All C. parvum isolates belonged to subtype family IIa. The susceptibility of adult rodents to C. parvum and sheep to C. muris has been proved experimentally. The first report of human infection with
Cryptosporidium pig genotype II was reported. While the occurrence of cryptosporidiosis in pig is breeding hygiene-dependent, in cattle it is breeding type-dependent.
Morphological variability of C. suis oocysts, studied using digital image analysis, revealed that the strains of C. suis oocysts in naturally infected pigs from farms in the Czech Republic were morphologically different from those originally described as C. suis.
AQUAPARA-OMICS: Aquatic parasitism meets biomics – addressing key biological questions using novel datasets and modern analytical tools.
Parasitism is one of the most successful lifestyles of living organisms. Despite the majority of parasites being aquatic, at least during part of their life cycle, comprehensive molecular datasets for them are still scarce. AQUAPARA-OMICS aims to explore the uncharted biodiversity of greatly undersampled groups of aquatic parasites such as the Myxozoa and Dicyemida, and monitor selected human and fish pathogens, by eDNA metabarcoding. Production of new genomic and transcriptomic datasets of basal neodermates, parasitic cnidarians and dicyemids will allow us to unveil their parasitic origin, evolutionary history and characterize unique and shared genomic traits. AQUAPARA-OMICS further aims to explore key genes and molecular mechanisms involved in parasite development, replication, survival strategies and host immune responses. This includes basic research related to the functional characterisation of candidate molecules for future studies on new therapies and vaccine developments, which are urgently required for emerging aquatic pathogens.
Czech Science Foundation – projects of excellence in basic research (EXPRO) (19-28399X; P.I.: T. Scholz; 2019–2023).
Chromosomal and molecular mechanisms of sex determination in Lepidoptera
Moths and butterflies (Lepidoptera) have sex chromosome systems with female heterogamety (WZ/ZZ, Z/ZZ), but the actual mechanism of sex determination is largely unknown. Only recently the primary sex-determining factor was discovered in the silkworm, Bombyx mori. Its W chromosome encodes the Fem piRNA, which promotes femaleness by downregulation of the expression of a Z-linked gene, Masculinizer, promoting male development in the W absence. However, results in wild silkmoths Samia cynthia spp. question the W role in determining female sex and support a Z-counting mechanism. On the contrary, our recent results suggest that the Fem piRNA/Masc pathway might be conserved in pyralid moths. Therefore, we study molecular mechanisms of sex determination in species with a stable WZ/ZZ system and those with dispensable or absent W. We identify orthologs of sex determining genes and analyse their expression and function using transcriptome sequences and available methods of molecular genetics. Our aim is to contribute to the understanding of the evolution of sex determination in Lepidoptera.
[PI: F. Marec]
Chromerid algae
Chromerids Chromera velia and Vitrella brassicaformis, alveolate algae isolated from Australian stony corals, are the main objects of our scientific interest (Moore & Oborník et al., 2008; Oborník et al., 2012). These algae are believed to represent the closest known phototrophic relatives to apicomplexan parasites (Moore & Oborník et al., 2008; Oborník et al., 2009; Janouškovec et al., 2010; Woo et al, 2015). We have so far studied chromerid ultrastructure, morphology, life cycles (Oborník et al., 2011, 2012), plastid genomes of both algae (Janouškovec et al., 2010) as well as their mitochondrial genomes (Flegontov et al., 2015). We have participated on the sequencing of nuclear genomes of chromerids as well (Woo et al., 2015). We suppose to continue with this research in the future.
Ecology of arboreal ants in tropical forest canopies
The canopies of tropical forest trees still belongs to the least known natural habitats in the world. However, arboreal insect species are rarely studied due to the limited access to the canopy and methods as canopy fogging. Its known that ants represent the majority of arthropod biomass in tropical forest canopies.
We use different methodological approaches a) single rope technique b) searching for the ant nests and foragers in fallen trees and c) construction of a special canopy ant bait stations to manipulate their activity in trees, and d) exposition and spatial translocation of articificial "bamboo" nests.
Aim of the project is to get a good understanding of the arboreal ant diversity and activity across different environmental gradients (successional and elevational changes), and to study the ant role in ant-herbivore-plant food-webs. In current project, we aim to perform also targeted manipulations of canopy ants to disentangle the effects of competition (species dominance), forest structure and climatic changes on their communities using the artificial nests and the observations at baits.
Funding:
2021-2023 Does competition really structure ant communities in tropical forest canopies? Czech Science Foundation (PI: P.Klimes)
2018-2020 Mobility Plus Grant among CAS and RBINS, Belgium (PI: P. Klimes)
2015-2021: European Research Council (GA669609, PI: V. Novotný).
2012-2014: Mechanisms structuring ant communities in the canopy of a tropical rainforest. Czech Science Foundation (PI: P.Klimes)
Key studies:
Klimeš P., Janda M., Ibalim S., Kua J. and Novotný V. (2011) Ecological Entomology 36: 94–103
Klimeš P., Idigel C., Rimandai M., Fayle T.M., Janda M., Weiblen G.D. and Novotny V. (2012) Journal of Animal Ecology 81: 1103-1112.
Plowman N.S., Mottl, O., Novotny, V., Philip F.J., Idigel, C., Rimandai M., Klimes, P. (2020). Nest microhabitats and tree size mediate shifts in ant community structure across elevation in tropical rainforest canopies. Ecography 43: 431–442.
Mottl O., Yombai, Fayle T.M., Novotny V., Klimes P. (2020) Experiments with artificial nests provide evidence for ant community stratification and nest site limitation in a tropical forest. Biotropica 52: 277-287.
Targeted mutagenesis in insects
Targeted mutagenesis is one of the key methods for functional gene analysis. Two methods of gene targeting were established for Drosophila by Rong and Golic (2000) and Bibikova et al. (2002). The first one is based on a pair of site-specific DNA modifying enzymes from yeast, a recombinase and endonuclease that release a linear DNA fragment containing a modified sequence of the target gene in primordial germ cells. The other method is based on custom designed zinc finger nucleases (ZFNs), which are chimeric enzymes consisting of a zinc finger DNA recognition domain and the nonspecific nuclease domain of the Fok I restriction enzyme (Kimet al. 1996).
We pioneered the first method in Drosophila by knockouting the entire gene family using homologous recombination. We also evaluated a simplified variant of the second method and used direct microinjection of custom-designed Zinc Finger Nuclease (ZFN) mRNAs into silkworm embryos. We have a world priority of using ZFNs to generate germline mutations in an insect species other than Drosophila.
Juvenile hormone receptor
Juvenile hormone (JH) is a terpenoid, a small lipophilic molecule of vital importance to insect development and reproduction. JH was so named for its capacity to block metamorphosis of larvae to adults: only when larvae attain an appropriate stage, a halt o fJH secretion permits metamorphosis. Larvae treated with JH fail to mature, and therefore compounds with JH activity serve as efficient insecticides. The molecular action of JH has for long decades remained an enigma, because a JH receptor could not be identified. In 1986, T.G. Wilson isolated a Drosophila mutant, named Methoprene-tolerant (Met) based on resistance to the JH-mimicking insecticide. The Met gene encodes a transcription factor of the bHLH-PAS family, which includes a receptor of the xenobiotic dioxin but no receptors of known hormones. Breakthrough data from our laboratory in 2007 showed that Met is required for JH to inhibit metamorphosis in the beetleTribolium: like depletion of JH itself, loss of Met caused precocious metamorphosis of the beetle larvae. Our current paper, published by PNAS, has finally brought conclusive evidence for the JH receptor role of Met. Based on structural modeling of the JH-binding domain of Met, we prepared a set of point mutations aiming to displace JH from the ligand-binding pocket. By testing these mutant proteins in vitro, we determined specific amino acids contributing to the high-affinity JH binding. Using mutants unable to bind JH, we demonstrated that recently observed interactions of Met with partner proteins require the specific ligand-binding capacity of Met. Therefore, Met resembles certain nuclear receptors, e. g., of retinoic acid or thyroid hormone, but since Met belongs to a different protein family, it establishes a prototype of a hormonal receptor of a novel class. Our results address a long-standing question of the mechanism of action of juvenile hormone and its insecticidal analogs.
Stress physiology of honey bees
The project focuses on the physiological processes that occur in bees when defensive anti-stress responses are triggered following intoxication with synthetic or natural toxins. The project concentrates on the investigation of vibroacoustic signals, their artificial intelligence-based analysis, and the correlation between these signals and biochemical traits like the level of nutrients, the activity of digestive enzymes, the level of oxidative stress, the composition of bee venom components, the level of stress hormones, the amount of vitellogenin in the haemolymph, and the amount of biogenic amines in the body of bees. The project's goal is to understand the physiological and pathological phenomena that occur in the bee's body during stressful situations and, if necessary, to apply them in practical beekeeping.
PI: Dalibor Kodrík
Survival in liquid nitrogen
The goal is to reveal biochemical and molecular mechanisms that allow diapausing larvae of drosophilid fly, Chymomyza costata to survive deep freezing and long-term cryopreservation in liquid nitrogen. Knowledge on principles of such extreme cold hardiness can serve as a basis for development of cryopreservation techniques for insects or other biological material. We believe that the extreme freeze tolerance of C. costata larvae is based on synergy of different mechanisms and, therefore, chose wide integrative approach including: (1) studies on how diapause, cold and drought acclimations alter metabolic pathways in larval tissues toward production and accumulation of innate cryoprotective mixture including amino acids, sugars, and other components. We are interested in how the cryoprotective mixture components affect dynamism of internal ice formation, stabilize proteins and protect them from loss of structure and activity, and protect the integrity of biological membranes; (2) analysis of adaptive changes in lipid composition of biological membranes, which affect the membrane fluidity and phase behavior and, consequently, allow maintaining barrier function at extremely low temperatures and upon freeze-dehydration; (3) search in C. costata genome for putative macromolecular cryoprotectants including heat shock proteins, ice binding proteins, and dehydration induced LEA-like proteins. We follow expression of their genes during acclimations, localize the protein products in tissues, and study their cryoprotective functions using artificial proteins produced in expression vectors.
New approaches to metabolite profiling in biological samples of animal origin
Multicomplex analysis of low molecular weight substances of diagnostic value has been a challenge in current metabolite research. This approach is promissing to getting an overview of the metabolic status and global biochemical events associated with a cellular or biological system. Our research aims are focused on high-end sample preparation and separaration procedures enabling comprehensive profiling of diagnostic compounds in complex biological, industrial and environmental matrices. Design and investigation of novel haloformates and their implementation in rapid, fast and reproducible analytical protocols have result in a comprehensive portfolio of unique analytical methods for a wide range of compound classes involving polyols, lipids, amines, organic acids, small peptides and steroids. The developed analytical protocols have been integrated with a house-made Metabolite Mapper tool enabling automated peak detection, metabolite library searching, component matrix formation and data exports for further data mining and statistical processing.
Adaptive behavior and population dynamics
Understanding the effects of adaptive behavior in interaction webs is important in the search for mechanisms that maintain ecosystem structure and biodiversity. Our research focuses on mathematical modelling of the interplay of adaptive animal behavior and population dynamics. Behavioral aspects such as changes of prey behavior under predation risk, adaptive habitat selection, optimal foraging, have been shown to strongly affect dynamics, stability, and persistence of populations. Using methods of the evolutionary game theory we study complex feedbacks between adaptive behaviors and stability and persistence of simple interaction networks including both negative (e.g., predation, competition) and positive (e.g., pollination) interactions.
New alternative approaches in pest control of the horse-chestnut leafminer Cameraria ohridella
New data on applicability of entomopathogenic fungi against important insect pest of the horse-chestnut leafminer Cameraria ohridella will be obtained. It will be verified if the fungi have any negative effects on biodiversity of the leafminer parasitoids.
Large-scale patterns of insect diversity in tropical rainforests
We study changes in species composition (beta diversity) and food web structure on large geographical scales (across hundreds of kms), both within relatively homogeneous lowland rainforest habitats and along major environmental gradients, including altitudinal. Our studies documented low beta diversity of insect herbivores within large areas of tropical lowland forests in New Guinea, while our ongoing study along a complete rainforest altitudinal gradient (from 200 to 3700 m asl.) indicates large species turnover with altitude of several insect taxa. This study is also paralelled by molecular analyses of differentiation among conspecific populations of insects with distance. Key papers: Novotny et al. (2007, Nature 448, 692-5), Craft et al. (2010, PNAS 107, 5041-6).
Phylogeny of butterflies as a tool for understanding of evolution of Ecological phenomena
Butterflies rank among best known groups of insects. Life history, habitat requirements,
seasonal occurrence and other details are known for most of European species, but many
phenomena are tractable only with understanding the evolutionary history of entire
monophyletic groups, typically genera. Our phylogeny analyses contributed to elucidating the
evolution of seasonal polyphenism of European map butterfly (Fric et al. 2004, J. Evol. Biol.),
the evolution of parasitic myrmecophily in Large blues (Pech et al. 2004, Cladistics; Fric et
al. 2007, Syst. Entomol.). Ongoing research targets the complex radiation patterns in Erebia
satyrines, dwellers of northern and mountain areas of Northern hemisphere.
Pollination biology in Afromontane ecosystems
Interactions between flowering plants and their pollinators and other visitors belongs to the keystones of (not only) communty ecology. We focus on biology of pollination in overlooked Afrotropical ecosystems with a large lack of studies. By detailed studying of pollination systems of individual plant species, we have convincingly shown how the results of many current studies can be misleading for understanding of the real relationships in communities due to some current methodological approaches. Recently we have started to focus on studies of general patterns in pollination networks and their changes along environmental gradients. Because of the multi-disciplinarity of pollination biology, we focus on biology of plants and bird pollinators as well.
Key publications: Janeček et al. 2011 Oikos; Padyšáková et al. 2013 PLoS ONE; Bartoš et al. 2015 Arthropod-Plant Interactions
HYDROLYZE: Innovative utilization of hydrolysate from animal waste for improvement of agricultural soil quality
Technology Agency of the Czech Republic (TA ČR), principal investigator, 2023-2025
The project aim is to test a new type of bioadditive, hydrolysate from animal waste, in order to protect physical, chemical, and biological properties of agricultural soils and decrease greenhouse gases emissions. The main aim is to test the efficiency and longevity of hydrolysate phase and dose in improving the soil quality and health. The secondary aim is to verify the efficiency of hydrolysate in the stabilization of plant biomass from harvesting remnants in the soil and in decreasing greenhouse gases emissions from the soil. All this will be tested considering the type of soil and crop ensuring their sustainability, maximum water retention, plenty of nutrients and microbial communities.
Habitat requirements of model species
Many threatened species have very localized distribution or are confined to a few sites. Despite their threatened status, the biology and habitat requirements of such species are not always fully understood. We assess habitat preferences of model species that often serve as indicators or umbrella species for biodiversity of certain group of organisms or habitats. Our studies help identifying potential risks for survival of local populations of the model species or other associated organisms and contribute to develop decision rules for conservation management.
Related publications:
Platek et al. 2019: When is a tree suitable for a veteran tree specialist? Variability in the habitat requirements of the great capricorn beetle (Cerambyx cerdo) (Coleoptera: Cerambycidae). European Journal of Entomology.
Kostanjsek et al. 2018: Size matters! Habitat preferences of the wrinkled bark beetle, Rhysodes sulcatus, the relict of European primeval forests. Insect Conservation and Diversity.
Insect seasonality:
Photoperiodic timer and mechanisms regulating insect Diapause
Our major interest is diapause and its regulation, particularly seasonal switch depending on day-length measurement called photoperiodic timer (clock). Our goal is identifying architecture of photoperiodic timer at the genetic, molecular and anatomical levels. We mostly use two insect species: Pyrrhocoris apterus (Heteroptera) and Chymomyza costata (Diptera).
Pyrrhocoris apterus (Heteroptera) undergoes adult reproductive diapause, which is characterized by absence of Juvenile Hormone synthesis.
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Using gene silencing in P. apterus, we confirmed the role of the circadian clock genes in photoperiodic timer (Kotwica-Rolinska et al., 2017).
- Using P. apterus, we described plasticity in Juvenile Hormone (JH) reception, where one universal receptor protein (MET) interacts with various partners in tissue specific manner (Smykal et al, 2014). One of responses requires interaction of MET with circadian proteins and output relies on novel, non-cyclical feedback between Par domain protein 1 and Cryptochrome (Bajgar et al., 2013a; Bajgar et al., 2013b).
- Surprisingly, JH not required for male mating behavior or fertility, whereas circadian genes are needed for the photoperiod-dependent switch from diapause to reproductive growth of MAGs and for mating (Urbanova et al., 2016)
Drosophilid fly Chymomyza costata undergoes photoperiodically regulated larval diapause.
- With robust photoperiodic diapause and adaptaion to temperate regions, Chymomyza costata is an interesting species to study circadian clock (Dolezel, 2019).
- Using RNAseq technology, we characterized transcription profiles associated with photoperiodic diapause induction. Short day photoperiod triggering diapause was associated to remarkable inhibition of 20-hydroxy ecdysone (20-HE) signalling during the photoperiod-sensitive stage of C. costata larval development (Poupardin et al., 2015).
- Using cell culture assays, we defined molecular mechanism of non-diapause (npd) mutant strain in C. costata. The 1855 bp deletion in npd strian removes crucial regulatory cis-elements as well as the minimal promoter, being subsequently responsible for the lack of tim mRNA expression (Kobelkova et al., 2010).
Representative publications:
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Smýkal V., Pivarči M., Provazník J., Bazalová O., Jedlička P., Lukšan O., Horák A., Vaněčková H., Beneš V., Fiala I., Hanus R., Doležel D. (2020) Complex evolution of insect insulin receptors and homologous decoy receptors, and functional significance of their multiplicity. Molecular Biology and Evolution 37 : 1775-1789. DOI: 10.1093/molbev/msaa048
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Kotwica-Rolinska J., Pivarčiová L., Vaněčková H., Doležel D. (2017) The role of circadian clock genes in the photoperiodic timer of the linden bug, Pyrrhocoris apterus, during the nymphal stage. Physiological Entomology 42 : 266-273.
DOI: 10.1111/phen.12197 - Urbanová V., Bazalová O., Vaněčková H., Doležel D. (2016) Photoperiod regulates growth of male accessory glands through juvenile hormone signaling in the linden bug, Pyrrhocoris apterus. Insect Biochemistry and Molecular Biology 70: 184-190. DOI: 10.1016/j.ibmb.2016.01.003
- Doležel D. (2015) Photoperiodic time measurement in insects. Current Opinion in Insect Science 7: 98-103. DOI: 10.1016/j.cois.2014.12.002
- Poupardin R., Schöttner K., Korbelová J., Provazník J., Doležel D., Pavlinic D., Beneš V., Koštál V. (2015) Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata. BMC Genomics 16: 702. DOI: 10.1186/s12864-015-1907-4
- Smýkal V., Bajgar A., Provazník J., Fexová S., Buřičová M., Takaki K., Hodková M., Jindra M., Doležel D. (2014) Juvenile hormone signaling during reproduction and development of the linden bug, Pyrrhocoris apterus. Insect Biochemistry and Molecular Biology 45: 69-76.
- Bajgar A., Jindra M., Doležel D. (2013) Autonomous regulation of the insect gut by circadian genes acting downstream of juvenile hormone signaling. Proceedings of the National Academy of Sciences of the United States of America 110: 4416-21.
Molecular pathogenesis of alimentary infection by tick-borne encephalitis virus
(Czech Science Foundation, 2023-2025, Co-P.I. Jiří Salát)
Biology, phylogeny and evolution
For historical reasons, current myxozoan taxonomy is based predominantly on the morphology and structure of the spores produced in the vertebrate (fish) host. However, phylogenetic relationships among the myxozoans based on different gene regions disagree with the traditional taxonomic classification: a number of myxosporeans with very similar spore morphology and belonging to the same genus were found to be phylogenetically distantly related, rendering most genera non-monophyletic. But how important is spore morphotype for the evolution of these highly reduced parasites? One of our principal aims is to investigate differences with regard to parasite development as well as life cycles and biology, in order to be able to understand why they cluster in different branches of the phylogenetic tree. By reconstructing the evolutionary history of myxozoans and their hosts, using dated metazoan trees and cophylogeny methods, we have recently demonstrated that myxozoans emerged approx. 700 mya and that they first invaded invertebrate hosts before including vertebrate hosts into their life cycles (Holzer et al. 2018, Mol Ecol 27:1651-1666). Following vertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogentic lineages. We identified the acquisition of vertebrate hsots that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. We currently study the beginning of the heteroxenous life cycle in myxozoans in old vertebrate hosts (Chondrichthyes and Agnatha; Lisnerová et al. 2020, Biology 9:10; Kodádková et al. 2015, Int J Parasitol 45:269-276) and try to understand how the secondary host was integrated into the life cycle of these parasites. The identification of characters and key events in myxosporean evolution lead to a better understanding of the broad diversity of modern species.
New Biorational Methods Applied to Control Selected Pests as an Alternative to Chemical Pesticides to Prevent Contamination of Soil and Water Resources
Our joint project with Israel aims to reduce the use of broad range pesticides applied to the soil by developing and evaluating technologies for controlling key pests in garlic and onion cropping systems, important crops in both countries. Entomopathogenic nematodes (EPN), fungi (EPF) and additional bio-rational practices will be applied to control plant parasitic nematodes, pathogenic fungi and pestiferous arthropods which negatively impact the quantity and quality of garlic and onion yields, thereby reducing pesticide use and respective contamination of soil and water resources. Additionally we aim to evaluate the effect of these environmentally sound practices on the biodiversity of the acarine soil fauna.
Funding: Ministry of Education, Youth and Sports; grant No. 8G15006 (PI: Z. Mráček/R. Zemek).
Key outputs:
Konopická J., Bohatá A., Palevsky E., Nermuť J., Půža V., Zemek R. (2022) Survey of entomopathogenic and mycoparasitic fungi in the soil of onion and garlic fields in the Czech Republic and Israel. Journal of Plant Diseases and Protection 129: 271-281.
DOI: 10.1007/s41348-021-00557-5
Konopická J., Bohatá A., Nermuť J., Jozová E., Mráček Z., Palevsky E., Zemek R. (2021) Efficacy of soil isolates of entomopathogenic fungi against the bulb mite, Rhizoglyphus robini (Acari: Acaridae). Systematic and Applied Acarology 26: 1149–1167.
Unveiling Tick Symbiosis: A Functional Dive into Tick-Bacteria Partnerships
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Developing "apo-symbiotic" ticks: We utilise ex vivo blood-feeding systems with antibiotic-treated blood meals to create ticks devoid of their bacterial symbionts. This allows us to compare "symbiont-free" and "symbiont-harboring" cohorts of ticks and understand the impact of these partnerships.
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Focus on key model systems: We primarily study the partnership between the bacterium Midichloria mitochondrii and the European tick Ixodes ricinus, but also explore symbiosis in Francisella and Ornithodoros ticks. This comparative approach provides valuable insights into function of diverse tick-symbiont interactions.
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How do symbionts influence tick development, reproduction, and feeding success?
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What role do symbionts play in tick immunity and defense against pathogens?
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Can understanding these partnerships pave the way for novel tick control strategies that target the tick-symbiont relationship?
PMID: 35810301
PMID: 32457850
Diplonemids
The aim of this project is to dedicate for the first time diplonemids to systematic and multifaceted research that will address their diversity, ecology, life style, genome and transcriptome, followed by functional studies of selected mitochondrial (mt) proteins. Based on the sequences gained from the latest studies of eukaryotic diversity in world oceans, diplonemids represent the 7th most abundant and 3rd most diverse group (de Vargas et al., Science 348: 1261605), but we do not even know how these cells look like. Our aim is to:
1/ study diplonemids in as many oceanic samples as possible, with the aim to establish their abundance and diversity, and gather data about their life cycle, stages, strategy and morphology;
2/ establish a representative species/strain as a new model organism that will allow to shed light on their amazing evolutionary success in contemporary oceans.
Via these aims, we want to uncover the potentially fascinating biology of these important organisms, which are arguably the least studied group of globally abundant eukaryotes. Initially, we will analyze all aspects of the metabarcoding data from the Tara Oceans and other expeditions, including our own, with the aim to map the phylogeny and diversity of diplonemids, their distribution, abundance and morphology, and statistical analysis of their co-occurrence with other marine prokaryotes and eukaryotes. The next step will be to get representative(s) of the most dominant and widespread clades into the culture, since D. papillatum, the only species studied in some detail so far, falls into the least ecologically and evolutionary relevant clade. The cultured strain(s) will be subject to whole genome sequencing with downstream analyses, such as the assembly and annotation of both mt and nuclear genomes, and analysis of the transcriptome(s), as well as detailed morphological analyses. Possibly the most challenging part of the project will be to turn the cultured strain into a genetically tractable model. Planned functional studies of the mt RNA processing machinery will be adjusted to how successful the previous step will be. However, even if we fail to genetically modify diplonemids, protocols will be applied that allow studying this unique machinery in wild type cells. Moreover, we expect that exciting and unanticipated findings will arise from the genome information.
Role of the only tRNA intron in trypanosomatids
In yeast Saccharomyces cerevisiae and other model organisms, 20% of all tRNAs contain introns. Their removal is an essential step in the maturation of tRNA precursors. In T. brucei, there is only one intron containing tRNA: tRNATyrGUA. Since this tRNA is responsible for decoding all tyrosine codons, intron removal is essential for viability. Using molecular and biochemical approaches, several non-canonical editing events were identified within the intron-containing tRNATyrGUA. The RNA editing involves guanosine-to-adenosine transitions (G to A) and an adenosine-to-uridine transversion (A to U), which are both necessary for proper processing of the intron. We have been obtaining tRNA intron sequences from our collection of newly identified trypanosomatid species. We hope this will help us to understand the process of RNA editing and ultimately identify biological function for the presence of the only intron containing tRNA in these organisms.
T. brucei bloodstream form mitochondrion: a key player in the parasite bioenergetics and metabolism
For the last 50 years, the bioenergetic dogma of the infectious stage of the human pathogen Trypanosoma brucei has been that the mitochondrion is an ATP-consuming organelle and that glycolysis is the sole source of cellular ATP.
We have shown that under certain environmental or genetic conditions, the mitochondrion of the bloodstream is capable of producing ATP via the substrate phosphorylation pathway.
Our discovery opens new opportunities to study mitochondrial metabolic pathways to redefine the metabolic role of the parasite mitochondrion.
We hope that our findings will open new opportunities for drug development and explain the molecular mechanisms behind the mode of action and drug resistance of commonly used drugs that accumulate in the parasite mitochondrion.
Microsporidia and Cryptosporidium of wild great apes
Projekt: Microsporidia and Cryptosporidium of wild great apes
Unraveling the diversity of parasites of cypriniform fishes in North America: a key to understand evolutionary processes.
The principal scientific goal of the project is to investigate the unknown diversity of two model groups of helminth parasites of cypriniform fishes (Cyprinidae and Catostomidae) in North America using (i) ectoparasitic monogeneans of the genus Dactylogyrus with direct life cycle and high host specificity, and (ii) endoparasitic flatworms (tapeworms of the order Caryophyllidea) with complex life cycle and lower degree of host specificity. For both parasite groups, their origin, host-parasite coevolution and historical biogeography will be studied. Another important goal is to contribute to career development of young Czech researchers and formation of a new generation of fish parasitologists in North America.
Ministry of Education, Sports and Youth – program Inter-Excellence (LTAUSA18; P.I.: T. Scholz; 2019–2022).
Population genetics, demography and molecular evolution in rodents and their parasites
Adaptive and co-speciation components of host-parasite coevolution are studied in rodents and their parasites. Two rodent groups (voles and wood-mice) and their ectoparasites (lice, mites) were selected as the model groups. Population structure is being analysed using mitochondrial genes and SNP profiling. Despite observing lineages with relatively strict degree of host specificity, only limited amount of co-speciation was seen in both parasitic groups. Hence, the adaptive component of evolution seems to be the major driver defining genetic differentiation. Currently, a newly discovered secondary contact zone in the louse Polyplax serrata (but lacking a corresponding SCZ in its host) is being explored using WG sequencing (P.Is.: V. Hypša and J. Štefka).
Eustigmatophyte algae
It is well known that eustigmatophytes lack chlorophyll c in their photosynthetic complexes, although it is a pigment hallmark of algae with secondary red plastids. The same pigment deficiency we found in chromerid algae Chromera velia and Vitrella brassicaformis (Moore & Oborník et al., 2008; Oborník et al., 2012). In frame of sequencing of the plastid genome of Trachydiscus minutus, a new star on the biotechnology sky of production of polyunsatrurated fatty acids, we tested a hypothesis concerning tertiary origin of chromerid plastid. When the similar (C. velia) or even identical (V. brassicaformis) pigment composition in chromerids and eustigmatophytes is taken into account, it is likely and phylogenetics analyses support this idea that chromerid plastid is derived from eustigmatophyte through a tertiary endosymbiosis (Ševčíková et al., 2015).
Diversity and biology of planktonic diplonemids
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Do entomopathogenic fungi drive arthropod diversity gradients via host negative density dependence?
Using a combination of field observations and experiments, we aim to quantify importance of
entomopathogenic fungi for the origin and maintenance of arthropod diversity in relation to
elevation, anthropogenic habitat change, and future climate change.
Funding: Czech Science Foundation 21-06446S (2021-2023, PI: Tom Fayle)
Lyme disease transmission model
GACR 13-12816P (2013-2015)
Lyme borreliosis is an emerging vector-borne disease of temperate climates, with a current distribution spanning North America and Eurasia. It is caused by spirochetes belonging to the Borrelia burgdorferi sensu lato group that are transmitted through Ixodes ticks. Although Lyme borreliosis is one of the best studied tick-borne zoonoses, the annual incidence leads other vector-borne diseases and continues to increase. There is currently no vaccine available to prevent Lyme disease in humans. One of the promising strategies to break Borrelia transmission is to develop of a vaccine affecting basic physiological processes of the tick. Development of a promising vaccine against Lyme borreliosis would be greatly facilitated by a reproducible vector host transmission model. Main aim of this project is to implement such model and to find a molecule with proven anti-borrelial effect.
Extracellular adenosine and its receptor
Adenosine is a multifunctional nucleoside that is most important as an intracellular precursor of nucleic acids and ATP, but it is also a key extracellular signaling molecule affecting a variety of cellular processes. The interest in adenosine as a signaling molecule goes back at least as far as 1929. It has been known since the early study of Drury and Szent-Gyorgyi that adenosine injection increased coronary blood flow, reduced heart beat rate and lowered systemic blood pressure (Drury and Szent-Gyorgyi, 1929). In later studies, the extracellular adenosine was also implicated in the regulation of immune and neural functions, as well as in the responses to stress and hypoxia.
Four mammalian subtypes of the AdoR have been identified and their genes cloned: A1, A2A, A2B, and A3. They have been shown to modulate intracellular levels of 3', 5'-adenosine cyclic monophosphate (cAMP) in different ways: A1 and A3 inhibit adenylate cyclase, whereas A2A and A2B stimulate this enzyme (van Calker et al., 1979; Londos et al., 1980). The existence of four receptors with different functions but overlapping patterns of expression, together with the pervasiveness of adenosine- mediated physiological events, pose difficult questions in efforts to design pharmacological and biochemical interventions (Nyce, 1999).
By conducting BLAST searches of the available Drosophila protein database, we have identified CG9753 as the gene encoding the Drosophila AdoR homolog. The sequence of Drosophila AdoR is quite divergent from the mammalian AdoRs but they still share the region important for adenosine binding. Furthermore, our pharmacological experiments revealed that Drosophila AdoR functionally responds to adenosine and is able to activate at least two second messenger pathways, involving cAMP and calcium. By assaying cAMP and Ca2+ levels in CHO cells transiently transfected with Drosophila AdoR, we detected increase in both cAMP and calcium levels after adenosine treatment. In both cases, activation occurred at physiologically relevant doses, and was only present for the AdoR plasmid in sense orientation.
Interaction between bZIP proteins Jun and Atf3 in epithelial morphogenesis during metamorphosis
Movements, fusions and closures of epithelial tissues are important for animal development, e.g. during embryogenesis but also for healing of wounds. The fruit fly, Drosophila melanogaster, offers several model examples of such epithelial movements and fusions. An interesting case is the formation of the adult fly abdomen. During metamorphosis of a maggot into fly, large larval epidermal cells (LEC) must leave the epithelium to free space for new cells (histoblasts), which rapidly proliferate and migrate to occupy the entire surface of the abdomen, then produce the adult cuticle. Regulation of this complex exchange of cell populations is unclear. It has been known that the entire process, like metamorphosis of other tissues, is stimulated by the steroid hormone ecdysone, and that the extrusion of LEC requires cytoskeleton changes dependent on the Rho signaling pathway. Unexpectedly we have implicated in the abdominal morphogenesis Atf3, a transcription factor of the bZIP family. Activity of the atf3 gene must be restricted during the exchange of the two cell populations, as deregulated atf3 blocks removal of LEC from the epithelium by interfering with Rho signaling and increasing LEC adhesiveness. These obsolete larval cells consequently obstruct closure of the adult epithelium. To exert this effect, Atf3 requires its binding partner, the oncoprotein Jun. Although interaction between these two regulatory proteins has been well documented by in vitro studies on mammalian cell lines, our results for the first time demonstrate a developmental function of the Atf3-Jun complex in vivo.
Molecular differentiation and evolutionary history of sex chromosomes in Lepidoptera
Sex chromosomes and their differentiation belong to most interesting questions of evolutionary genetics. In animals, overwhelming majority of data on the sex chromosome evolution were obtained in organisms with male heterogamety (i.e. with XY sex chromosome systems) such as flies and mammals. Much less is known about organisms with female heterogamety, possessing a WZ sex chromosome system or its variations. This particularly regards moths and butterflies (Lepidoptera), the largest animal group with female heterogamety. In selected models we study physical features of lepidopteran genomes, perform synteny mapping of conserved genes, and examine molecular differentiation of sex chromosomes with the aim to uncover evolutionary history of lepidopteran karyotypes and contribute to understanding general mechanisms of sex chromosome evolution.
[PI: F. Marec]
Function of bee venom toxins
The project focuses on the individual components that make up bee venom, especially melittin and phospholipase A2, which are the most abundant elements of the venom and the main contributors to pain and allergic reactions brought on by bee stings. They have also demonstrated in vivo anti-bacterial, anti-tumour, and anti-inflammatory activity. The ratio of representation of individual components in the venom and environmental influences, such as exposure to toxic substances in the form of insecticides or stress brought on by the presence of predators or pathogens in the bee colony, are investigated using molecular methods (primarily RT-PCR). Additionally, it is being researched whether the bee organism can use the venom's components for its own defence during an infection immune response or as an anti-stress reaction when the organism's integrity is compromised.
PI: Markéta Hejníková
Insect overwintering as limiting factor for poleward spread
Insects have successfully colonized almost all terrestrial ecosystems and this success is closely associated with their remarkable adaptations to endure climatic extremes. Even so, insect distributions are currently changing rapidly in response to climate change. The project address questions related to the physiological limits and/or drivers of insects' poleward colonization of colder habitats from tropical hotspots. We focus on overwintering stage of insect life cycle in select models (e.g. adults of linden bug, Pyrrhocoris apterus) and ask what exactly the environmental factors are that limit the winter survival of their populations. In addition to the apparent and often considered low temperature extremes, we study the effects of microhabitat temperature buffering, moisture and risk of ice nucleation, repeated bouts of freezing and melting, ice recrystallization, warm spells that may cause cold de-acclimation and energy depletion on one side, but repair of chronic cold injury on the other side. In addition to analyzing select insect species in detail, we exploit the family of drosophilid flies that offers ideal model system of more than 1 500 species (many of them readily available and easy to maintain in laboratory) that represent the evolutionary journey from original tropical-African habitats to the species which are now firmly established in sub-Arctic regions. We analyze metabolic responses in different species to various levels of cold stress ranging from brief cold shock and short-term quiescence to long-term acclimation including diapause induction and exposure to subzero temperatures to find whether there are any stereotypic metabolic patterns (e.g. accumulation of typical osmolytes) that would underlie the capacity of species to tolerate the cold stress and, consequently, to colonize the colder habitats.
Dynamics of structured populations
Many practical and theoretical problems in ecology, epidemiology and evolutionary biology require consideration of a type of population structure. For example, analyzing impacts of efficiency of a variety of age-specific interventions or of vaccine prioritization in the ongoing COVID-19 epidemics, as well as exploring changes in dynamics of animal populations subject to sexually transmitted infections or sex-selective predators, we need to structure the respective populations by age and sex, and mirror this structure in the corresponding mathematical models. Our current research in this respect covers a range of topics, including dispersal-driven metapopulation dynamics, impacts of mating strategies on dynamics of populations subject to sexually transmitted infections, evolution of life history in age-structured or sex-structured populations, and actually exploration of impacts of non-pharmaceutical interventions and vaccination strategies on dynamics of the COVID-19 epidemic. Our results have ramifications for conservation strategies, biocontrol programmes, and generally management of populations.
Forest dynamics in a tropical rainforest
We are in the middle of the first survey of our 50-ha permanent forest dynamics plot in lowland rainforest near Wanang Village in Papua New Guinea. We will map, tag and identify all stems more than 1 cm in diameter, approximately 270,000 stems in total. This plot (surveyed in collaboration with G. Weiblen, University of Minnesota) is a part of the global network of forest dynamics plot coordinated by the Center for Tropical Forest Science. It is so far the only such plot east of Wallace's line
Ecology and conservation of butterflies in traditional managed landscape
The EU-protected Marsh fritillary still persists in strong populations in westernmost areas of the Czech Republic. Following its populations from 2002 onwards resulted into detailed understanding of its habitat requirements (Konvicka et al. 2003, EJE) and management needs (Hula et al. 2004, Entomol. Fenica). Our active involvement in the species conservation included designing NATURA 2000 sites, drafting a species action plan, and advisory participation in habitat management. Several publications used this endangered species as a model for studies of dispersal (Fric & Konvicka 2007, Basic and Applied Ecology) and metapopulation structure (Fric et al. 2010, Ecol. Res.) of butterflies inhabiting seminatural grasslands.
SOMForClim: Soil organic matter fractions and soil carbon storage as affected by forest type and climate change
Czech Science Foundation (CSF), principal investigator, 2022-2024
Temperate forests hold a great potential for storing soil organic C (SOC). The bulk SOC, however, is partitioned into fractions of soil organic matter (SOM) that differ in terms of formation, persistence, and function. As a result, the fractions might be differently affected by carbon (C) input chemistry (quality) and climate change. Here, we compare the amounts of C in SOM fractions among deciduous, coniferous, and mixed forest soils along the soil profile. We also determine how the formation and persistence of SOM fractions are affected by C input quality (i.e., litter leachates vs. root exudates), increased temperature, and soil fauna and microorganisms. The proposed project consists of field samplings and observations, a slightly manipulated field experiment that explains a part of the process, and two heavily manipulated laboratory experiments that explain the process in detail. Finally, the acquired data will be compiled and used to improve and validate selected soil C models.
Ecology of butterflies and moths in Afrotropical ecosystems
Butterflies and moths (Lepidoptera) belong to the traditionaly most studied groups in community ecology, knowledge of their biodiversity in tropical Africa is, however, still insuficient. We focus mainly on patterns in their species and functional diversity along environmental gradients, currently in the model locality of Mt. Cameroon. Simultaneously we study also other factors, such as impact of forests structure and disturbances on lepidopteran communities with applications into practical conservation of tropical biodiversity. We use lepidopterans also as an important model in our pollination studies. Last but not least, we do not forget to basic knowledge of African Lepidoptera, including taxonomy, phylogeny and natural history.
Population ecology, dispersal, and phylogeography
Animal movement and demographic structure are some of the key parameters affecting the survival of local populations, and thus they have become of particular interest for conservation biology of the threatened species. Using relevant approaches (e.g. mark-release-recapture or radio-tracking) we study population structure and dispersal of endangered beetles, with the main focus on Rosalia alpina and Cerambyx cerdo. Further, to better understand the genetic population structure and the evolutionary history of these species, we also employ molecular methods commonly used in ecological studies. Our findings are important for designing more efficient conservation strategies.
Related publications:
Drag & Čížek 2018: Radio-Tracking Suggests High Dispersal Ability of the Great Capricorn Beetle (Cerambyx cerdo). Journal of Insect Behavior.
Drag et al. 2018: Phylogeography of the endangered saproxylic beetle Rosalia longicorn, Rosalia alpina (Coleoptera, Cerambycidae), corresponds with its main host, the European beech (Fagus sylvatica, Fagaceae). Journal of Biogeography.
Phylogeography
Publications:
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Ditrich T., Janda V., Vaněčková H., Doležel D. (2018) Climatic variation of supercooling point in the linden bug Pyrrhocoris apterus (Heteroptera: Pyrrhocoridae). Insects 9 : article number 144.
DOI: 10.3390/insects9040144 - Pivarciova, Provaznik, Vaneckova, Pivarci, Peckova, Bazalova, Wu, Cada, Kment, Kotwica-Rolinska, Dolezel: Unexpected geographic variability of free running period in the linden bug, Pyrrhocoris apterus (Journal of Biological Rhythms, DOI: 10.1177/0748730416671213)
Publication connected to geographic variability, but on a different insect model:
- Paolucci S., Dalla Benetta E., Salis L., Doležel D., van de Zande L., Beukeboom L.W. (2019) Latitudinal variation in circadian rhythmicity in Nasonia vitripennis. Behavioral Sciences 9 : article number: 115. DOI: 10.3390/bs9110115
Geographic adaptations of the linden bug, Pyrrhocoris apterus, and its phylogeography
We use our favorite model organism, Linden bug (Pyrrhocoris apterus), to study diapause and particularly its photoperiodic regulation. Seasonal environmental changes are mostly influenced by latitude and altitude of particular locality. Indeed, we observe remarkable variability in photoperiodic and circadian clocks between geographical field-lines of P. apterus. Robust analysis of P. apterus phylogeography is needed to shed some light on origin of these adaptations. In collaboration with Prof. Roger Butlin (University of Sheffield) we are performing RAD sequencing and analysis of samples from approximately 150 localities.
Current collection of P. apterus (see the map) was only possible thanks to generous help of following colleagues: Adam Bajgar, Alejandro Cabezas-Cruz, Aleksandra Konjevic, Barbara Lis, Jerzy A. Lis, Carl-Cedric Coulianos, Rodolfe Costa, Dora Nagy, Eva Hola, Hanka Vaneckova, Iva Fukova, Jana Pavlová, Joanna Kotwica-Rolinska, Jula Lukes, Kai Schuette, Kajka Straznicka, Lucia Salis, Lukas Cizek, Lukas Drag, Manuel Baena, Marek Jindra, Marketa Ondrackova, Martin Kaltenpoth, Martin Vacha, Matilde Eizaguirre, Milan Stech, Milena Damulewicz, Olina Bazalova, Petr Kment, Petra Sekyrova, Plamen Kalushkov, Radka Zavodska, Ramon Albajes, Stanislav Rada, Teemu Rintala, Vlastimil Smykal, Xanti Pagola, Zejlko Popovic,
However, several geographical regions are either underrepresented or even absent completely (see red circles in the map below). Therefore, we would really welcome samples (either dead or alive) from following regions:
Europe – England, Sweden, Norway, Denmark, Mediterranean islands (Sicily, Corsica, Sardinia, islands in Aegean sea), Romania, Moldavia, Portugal, Belarus, Ukraine, Russia,
North Africa– Morocco, Tunisia, Algeria, Egypt
East – Turkey, Syria, Lebanon, Jordan, Iraq, Iran, Afghanistan, Pakistan, Oman, Saudi Arabia, Emirates, Georgia, Azerbaijan, Turkmenistan, Tajikistan, Uzbekistan, Kyrgyzstan, Kazakhstan, Russia, South West Mongolia, North West China
Sample collection: The optimal way for storing and transporting samples seems to be 96% ethanol (non-denatured). 2ml screw cup tubes can accommodate 5 - 8 bugs from the same locality. We are ready to send prepared tubes filled with EtOH, just send an e-mail request, please. Although we are happy even for one individual bug, 10-15 specimens from one locality are optimal. It is important to have the report of the locality (such as GPS position or locality name from the map, elevation is also very useful). Please, if possible, it would be also great to mention, if the locality was urbanized area (town, park and similar area modified by human) or if the locality is more similar to original nature-like type (forest, steppe, mountains). In ideal case we would like to have samples collected approximately 200 km apart in lowlands, while in mountains or complex terrain even higher density is helpful (down to tens of kilometers).
Living bugs – an alternative is to collect live specimens. Adults survive with wet piece of cotton or cellulose in small paper box for more than one week, as long as it is not too hot. We are really happy to obtain living specimens for establishing colonies, where circadian and photoperiodic phenotypes can be characterized.
Species identification - Pyrrhocoris apteruscan be quite easily identified thanks to its aposematic coloration. Both, larvae or adults can be collected and are welcome. We are also seeking for samples of closely related pyrrhocorids, such as P. sibiricus, P. marginalis, and genus Scantius (see the pictures below).
Contact: David Dolezel, david.dolezel@entu.cas.cz; Institute of Entomology; Biology center CAS; Branisovska 31; 370 05 Ceske Budejovice; Czech Republic
Evolution of symbiotic bacteria associated with arthropods
Tick-borne diseases in urban environments - where does the real danger lurk?
(Czech Health Research Council, 2023-2026, P.I.: Václav Hönig)
Arthropod Vectors of Raspberry Viruses
This project is part of a bilateral project with Norway „Healthy berries in a changing climate: development of new biotechnological procedures for virus diagnostics, vector studies, elimination and safe preservation of strawberry and raspberry“ which is lead by Dr. Jana Fránová. The aim of the project is to increase the production potential of berries in a new and challenging climate by using high-quality virus-tested mother plants, improving virus control approaches, well-study of associated vectors, and better safeguarding of valuable plant germplasm and plant health.
Funding: A € 1,450,000 grant from Iceland, Liechtenstein and Norway through the EEA Grants and Technology agency of the Czech Republic within the KAPPA Programme (PI: J. Fránová).
Key outputs:
Tan J., Trandem N., Fránová J., Hamborg Z., Blystad D-R., Zemek R. (2022) Known and potential invertebrate vectors of raspberry viruses. Viruses 14: 571.
Research and development of vaccine prototypes against Lyme disease
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produce in an E. coli expression system and purify native his-tagged nanovaccines, immunise mice, and efficiently (100% effective) block transmission of B. afzelii (local strain) from laboratory-infected I. ricinus nymphs to naïve mice.
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describe mechanistic understanding of the mode-of-action of the anti-OspA antibodies inhibit the B. afzelii spirochetes in the tick Ixodes ricinus and whether tick physiology and tick (immune) proteins contribute to the elimination of antibody-bound Borrelia.
Unveiling unknown myxozoan diversity and origins by eDNA
Due to their microscopic size, cryptic nature and their ability to switch between different invertebrate and vertebrate host groups, we know virtually nothing about the true diversity of Myxozoa. However, the transmission from host to host involves the release of durable spore stages in the environment. Following marker design for different myxozoan lineages, we are currently analyzing eDNA sequences generated by high throughput sequencing of water filtrates and sediments from marine and freshwater habitats. Special focus lies on Central European water bodies whose myxozoan fauna in fish is well described (funded by the Czech Science Foundation), but also on comparing marine habitats from different latitudes (financed by the Swedish Research Council). Using this approach we have discovered new phylogenetic lineages, which allow deeper insights into myxozoan evolution and may even clarify the question of marine vs. freshwater origin of Myxozoa. In this context, we also investigate previously unexplored host groups by analyzing vertebrate and invertebrate taxa that have escaped our attention as potential myxozoan hosts to date but are implied as such by evolutionary studies.
Non Stop Blastocrithidia: the trypanosomatids with all three stop codons reassigned
Genetic code previously thought to be universal for all the life forms but soon variations from canonical code were described in many organisms all across the tree of life, most of the deviation involves reassignment of one or two stop codon to sense codons leaving 1 or 2 stop codons to confer the termination of translation. Interestingly, in 2016 two groups of protist trypanosomatid Blastocrithidia and several ciliates were shown to reassign all the tree stop codons in their nuclear genome to code amino acids. Transcriptome and proteome analysis of Blastocrithidia revealed UGA has been reassigned to code tryptophan, while UAG and UAA are reassigned to code glutamate. This finding challenges our current understanding of very fundamental process of life “Translation”.
Blastocrithidia is an ideal organisms to study this phenomenon as it belong to well studied group of kinetoplastida where all the known kinetoplastids have canonical genetic code. We have successfully optimized the genetic manipulation of Blastocrithidia which will allow us to explore different aspect of translation.
Recent development in ribosome profiling which involves deep sequencing of ribosome protected mRNA fragment is a powerful tool for monitoring in vivo translation optimization of ribosome profiling and genetic manipulation of Blastocrithidia will allow us to address following questions: Qualitative and quantitative analysis of translation process, Biased in usage of canonical and non canonical synonymous codons, how does the termination of translation work without defined stop codon and evolution of genetic code.
Nuclear export of tRNAs in trypanosomes
Regulation of tRNA export from the nucleus to the cytoplasm might be an additional post-transcriptional event involved in gene regulation. However, our knowledge about tRNA export in trypanosomes is very limited. Although export factors of higher eukaryotes are reported to be conserved; only a few orthologs can be easily identified in the genome of T. brucei. Thus, we are going to employ methods of molecular biology and biochemistry to identify and characterize the tRNA export machinery in trypanosomes.
The role of ATP synthase structure in the biogenesis and bioenergetics
Mitochondrial cristae are inner membrane convolutions where protein factories responsible for bioenergy conversion reside. The cristae exhibit extremely large variability in their ultrastructure, except for one common attribute - the presence of ATP synthase dimer rows at the crista ridges. Little is known about the role of these arrays in cristae structure and mitochondrial bioenergetics. However, Trypanosoma brucei is an excellent model system as the singular mitochondrion of the digenetic parasite is drastically remodeled structurally and metabolically as it progresses through a complex life cycle. Notably, the highly branched, cristae-containing and ATP-producing mitochondrion transitions to a streamlined tubular, cristae-lacking and ATP-consuming organelle. Combining traditional biochemical methods with state-of-art structural approaches (single-particle cryo-EM), we solved the ATP synthase dimer structure, identified a dimer-specific subunit and explored its role in cristae shaping.
Now we aim to decipher the role of ATP synthase dimers in mitochondrial bioenergetics and biogenesis during the parasite differentiation.
Porcine cryptosporidiosis - Cryptosporidium scrofarum n. sp.
Previous molecular epidemiology and experimental infection studies revealed the susceptibility of pigs to a number of species including C. suis, C. parvum, C. hominis, C. felis, C. meleagridis, Cryptosporidium pig genotype II. We describe the morphological, biological, and molecular characteristics of Cryptosporidium pig genotype II and propose the species name Cryptosporidium scrofarum n. sp. to reflect its prevalence in adult pigs worldwide. The age susceptibility of pigs to C. scrofarum was experimently established on 5 week of age. Both C. suis and C. scrofarum is not associated with diarrhoea. Generally, C. suis is primarily detected among piglets up to 5 week of age, whereasC. scrofarumis dominant species in older and adult domestic pigs and as well as wild boars.
Trematodes in sub-Arctic lake food webs: development of quantitative diversity baselines and a framework for community ecology research in the Arctic.
The project is focused on increased resolution in assessments of host-parasite interactions in sub-Arctic freshwater ecosystems by an integrated framework for the discovery of trematode diversity. We aim to provide the first contemporary quantitative baselines for abundance and community structure in model host-parasite systems and to validate an ecological framework for future comparative studies in lake ecosystems of the sub-Arctic. A principal goal is to provide comprehensive baselines for trematode diversity and abundance in key fish and snail species in three model lake ecosystems in Iceland. Having established the genetic species diversity, we shall identify the composition and structure of parasite communities in the model lake ecosystems addressing key issues related to (i) parasite-parasite interactions in local food webs; (ii) host-parasite associations and recognition of host-parasite interaction networks; and (iii) development of quantitative baselines and assessment of the predictability of parasite populations and communities over different temporal and spatial scales.
Czech Science Foundation (18-18597S; P.I: A. Faltýnková; 2018–2020).
Development of generic strategies for the construction of genetic sexing strains in pest Lepidoptera
During the last 25 years, the Sterile Insect Technique (SIT) has been successfully implemented against several major lepidopteran pests. Programmes using SIT to control populations of these pests rely on bisexual releases. Male-only releases could significantly reduce costs and increase efficiency of SIT. However, a convenient genetic sexing system to produce male-only progeny is not yet available in any pest Lepidoptera. We are developing generic strategies for the construction of genetic sexing strains in Lepidoptera in two ways: (1) by inserting a conditional lethal gene into the female-specific W sex chromosome using genome editing to abort the development of female embryos, and (2) by identification of genes involved in sex determination with the aim to find new possibilities for genetic sexing. As the main model species, we use the codling moth, Cydia pomonella, which is a key pest of pome fruit and walnut orchards in the temperate regions of the world. This research is part of an international project co-ordinated by IAEA (Vienna, Austria).
[PI: F. Marec]
Synthesis of tetrapyrroles
Tetrapyrroles heme and chlorophyll are essential for life on Earth. We are interested in evolution of the heme biosynthetic pathway, particularly in origins of involved enzymes and their intracellular localizations. We focus mainly on algae that have passed through a process of secondary endosymbiosis, such as chromerids, dinoflagellates, diatoms and cryptophytes, and at the end also apicomplexan parasites. We showed that phototrophic alga C. velia produces 5-aminolevulinate similarly to apicomplexan parasites from glycine and succinyl CoA in the mitochondrion. All other eukaryotic phototrophs synthesize this precursor from tRNA-GLU in the plastid, where the entire pathway is located. We study heme pathway also in other organisms such as Vitrella brassicaformis, Bigelowiella natans, Paulinella chromatophora, Glenodinium foliaceum and others.
Network ecology in the big data age: understanding changes in species interaction specificity along environmental gradients
By collating a large number of existing interaction network datasets, we will explore changes in
interaction specificity along global-scale environmental gradients, including latitude, altitude and
habitat modification, accounting for network mid-domain effects and cascading extinctions.
Funding: 2019-2021 Czech Science Foundation 19-14620S (PI: Tom Fayle)
Fayle T.M., Sam K. Humlova A., Cagnolo L. & Novotny V. (2016) The LifeWebs project: A call for data describing plant-herbivore interaction networks. Frontiers of Biogeography 8.4: e31122
Babesiosis transmission model
Babesiosis is a tick-borne malaria-like disease of mammals. Because of global changes and expansion of the tick range, importance of babesiosis as an emerging zoonosis is increasing. Interplay between the parasite, the tick and the vertebrate host represent a complex system of multiple molecular interactions. To date, only a limited number of molecules have been identified to play a role in this system. Our research is focused on the identification and characterization of molecular mechanisms of Babesia persistence within the tick vector and its transmission to the vertebrate host. We are currently working on the setting of Babesia transmission model in our laboratory and use of this model for testing of the tick immune genes in Babesia infection by RNA interference.
Juvenile hormone: mechanism of action during insect metamorphosis
Metamorphosis of holometabolous insects such as beetles or butterflies is a marked change of form between juvenile and adult stages that enables the larva to efficiently utilize food sources and the flying adult to spread the species. The entry to metamorphosis depends on the morphogenesis-promoting ecdysteroids and the antagonistically acting juvenile hormone (JH), which precludes metamorphosis until a larva attains the appropriate size and developmental stage. JH has been known to prevent metamorphosis since the work of V.B. Wigglesworth for over 70 years. However, the mechanism of JH action has remained an enigma as neither a JH receptor nor its signaling pathway are known. By using the red flour beetle Tribolium castaneum, we showed that a gene Methoprene-tolerant (Met), originally uncovered as a mutation conferring resistance to JH in the fly Drosophila, mediates the anti-metamorphic JH effect. Loss of Met function renders Tribolium insensitive to JH and, unlike in Drosophila, it also causes the beetle larvae to metamorphose precociously. We further showed that in response to JH, Met controls metamorphosis by regulating expression of the Broad-Complex and Krüppel-homolog 1 (Kr-h1) genes, which play critical roles during larva-pupa and pupa-adul metamorphic changes. Our latest studies thus for the first time demonstrate the key role of Met in the regulation of insect metamorphosis by JH and support the disputed function of Met as a receptor or transducer of the JH signal. We have recently shown that this JH signaling pathway is functionally conserved in evolutionarily distant hemimetabolous insects.
Overwintering in insects of economic importance
We follow the course and the success of overwintering in insect pest species (or beneficial insects) in their field habitats. We assess the seasonal timings of diapause induction, initiation, termination and the onset of spring activity. We assess a whole set of physiological parameters, which correlate and/or are causally involved in cold tolerance and winter mortality. We use various techniques (supercooling point, vapour pressure and Clifton nanoliter osmometers, differential scanning calorimetry, gas exchange and respirometry analysis, high resolution mass spectrometry, etc.). Select target species: Ips typographus, Pityogenes chalcographus, Cydia pomonella, Ostrinia nubilalis, Culex pipines and others.
Ecophysiological limits of high mountain relics
Although there is general agreement that rare species of cold environments may be most severely impaired by ongoing climate change, the knowledge of precise mechanisms impairing such species is almost nonexistent. Until recently, most of research on insect thermal physiology focused on low-temperature limits of warm-adapted species, whereas cold-adapted species were neglected, partly due to difficulties with rearing such species in laboratory. We successfully developed methods of mass rearing of several high mountain butterflies (genera Colias, Erebia), and PhD student Pavel Vrba is recently experimenting with thermal limits of overwintering larvae, putatively the most sensitive stage.
The effect of soil fauna on carbon sequestration in extreme environments
European Cooperation in Science and Technology (COST), team member, 2017-2019
We aimed to determine the relative importance of respective groups of soil fauna in soil carbon sequestration not only in extreme environments, which, however, served as models for such processes. We were interested in estimation of relative proportions of soil organic matter fractions, which resulted from litter decomposition as affected by various functional groups of soil fauna. In situ enclosure experiments as well as lab manipulative experiments under controlled conditions were used.
Circadian clocks
Circadian clock - evolution, comparative studies
Circadian biological clocks are found in most living organisms and their fundamental properties are highly conserved in vertebrates and invertebrates. The fruitfly, Drosophila melanogaster served as a premier insect species for the molecular analysis of the circadian rhythms, and we enjoy using its powerful genetic tools as well (Singh et al., 2019). Because of the functional similarities of the circadian clocks among all metazoans, it was suggested that the molecular mechanisms underlying the clock function would be conserved as well. Surprisingly, we can see remarkable differences between the molecular regulations of the circadian timing system even among holometabolous insects. The long-term goal of our laboratory is to gain a better understanding of the cellular and molecular mechanisms that underlie circadian rhythmicity and to shed some light on evolution of circadian and photoperiodic clocks. We also explore role of circadian genes in a non-clock processes, i.e., in magnetoreception (Bartos et al. 2019, Bazalova et al., 2016).
Representative publications:
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Singh S., Giesecke A., Damulewicz M., Fexová S., Mazzotta G.M., Stanewsky R., Doležel D. (2019) New Drosophila circadian clock mutants affecting temperature compensation induced by targeted mutagenesis of timeless. Frontiers in Physiology 10 : article number: 1442.
DOI: 10.3389/fphys.2019.01442 -
Bartoš P., Netušil R., Slabý P., Doležel D., Ritz T., Vácha M. (2019) Weak radiofrequency fields affect the insect circadian clock. Journal of the Royal Society Interface 16 : article number: 20190285. DOI: 10.1098/rsif.2019.0285
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Bazalová O., Doležel D. (2017) Daily Activity of the Housefly, Musca domestica, Is Influenced by Temperature Independent of 3' UTR period Gene Splicing G3: Genes, Genomes, Genetics 7 : 2637-2649. DOI: 10.1534/g3.117.042374
- Bazalova O., Kvicalova M., Valkova T., Slaby P., Bartos P., Netusil R., Tomanova K., Braeunig P., Lee H.-J., Sauman I., Damulewicz M., Provaznik J., Pokorny R., Dolezel D., Vacha M. (2016) Cryptochrome 2 mediates directional magnetoreception in cockroaches.Proceedings of the National Academy of Sciences of the United States of America 113: 1660-1665. DOI:10.1073/pnas.1518622113
Neuropathogenesis linked to NS1 protein of tick-borne encephalitis virus
(Czech Science Foundation, 2023-2025, P.I. Martin Palus)
A model organism for myxozoan research
Functional research on myxozoan parasites is notoriously difficult and many aspects of their biology still lie in the dark. A major reason for the limited information is the absence of an in vitro model and the paucicity of in vivo models. Only a few life cycles are continuously perpetuated in research laboratories around the world, as their maintenance is laborious and time-consuming, with the production of fish-infective spore stages in oligochaete or polychaete cultures accounting for several weeks or months. We have recently established the first continuous in vivo model for myxozoan pre-sporogonic proliferative stages (Born-Torrijos et al. 2022, Cells 11: 377). The model employs Sphaerospora molnari, a common parasite of common carp, Cyprinus carpio (Eszterbauer et al. 2013, Dis Aquat Org 104:59-57). In natural infections, S. molnari invades the epithelia of skin and gills where it forms spores and causes marked dystrophic changes and necrosis. Prior to spore formation, S. molnari proliferates in the blood of carp, forming highly motile blood stages (Hartigan et al. 2016, Sci Rep 6:39039). Our research model focusses on this early intrapiscine development and overcomes the problems related to the duration of spore formation in invertebrate hosts, by transferring blood stages from fish to fish. We are also able to cultivate and multiply these stages over several days in vitro, and genomic and transcriptomic datasets are available to explore parasite and host genes. The model hence allows us to investigate stage-specific gene expression, host-parasite interactions, as well as the identification of potential therapeutic targets (Hartigan et al. 2020, BMC Genomics 21:404; Korytar et al. 2019, Parasit Vect 12:208; Korytar et al. 2020, Parasite Immunol 42:e12683).
Innovation of Integrated Potato Protection Against the Colorado Potato Beetle Based on New Knowledge of Genetic and Biological Characteristics
Colorado potato beetle (CPB) is our main pest in the above-ground mass of potatoes with the potential for crop losses up to 50%. However, protection against it is currently very difficult due to insecticide resistance. In addition to the use of chemical protection and controversial genetic modifications, the development and use of biological protective methods are becoming increasingly promising. Use of entomopathogenic fungi (EPF) and parasitic nematodes (EPN) for protection does not cause a pest resistance. A great advantage is the support in use of mycoinsecticides by sustainable and organic farming programs. Apart from conservation studies, molecular and genetics methods are used wordwide to address the invasive and genetic potential of CPB.
Funding: Ministry of Agriculture; Project NAZV ZEMĚ No. QK1910270 (PI: O. Skoková Habuštová).
Key outputs:
Konopická J., Skoková Habuštová O., Jánová N., Žurovcová M., Doležal P., Zemek R. (2024) Isolation and identification of entomopathogenic fungi strains for Colorado potato beetle (Leptinotarsa decemlineata) control Journal of Applied Microbiology lxae213.
Zemek R., Konopická J., Jozová E., Skoková Habuštová O. (2021) Virulence of Beauveria bassiana strains isolated from cadavers of Colorado potato beetle, Leptinotarsa decemlineata. Insects 12: article number: 1077.
Nutritional sensing of ticks
PI: Dr. Petr Kopáček, Dr. Jan Perner
GAČR: 18-01832S, 24-10659S
In this project, we address two highly intriguing but contrasting features of the parasitic lifestyle of ticks - the ability to ingest and digest enormous amounts of blood, and the ability to survive long periods of starvation between blood meals. The striking contrast between food surplus and scarcity must be tightly controlled by mechanisms of nutrition signaling and sensing. Using the European Lyme disease vector, the tick Ixodes ricinus, we will investigate the role of upstream components of the tick's insulin signaling pathway, specifically the tick's four insulin-like peptides and their putative antagonist Impl2. We will also functionally characterize the amino acid (leucine) sensing pathway leading to the activation of TORC1 in the tick and the role of the lysosomal v-ATPase in controlling the intracellular digestive machinery. The phenotypes obtained by RNA interference or chemical inhibition, as manifested by impairment of tick feeding or reproduction, will serve for future rational development of vaccines or preparations for effective tick control.
Research Articles:
PMID: 33706210
Evolution of trypanosomatids pathogenicity
Trypanosomatids undoubtedly belong to the most successful parasites on Earth with unique life style and ingenious adaptations to the hostile environment of the host. Because they cause devastating diseases and therefore represent major threat not only for developing countries, several dixenous (two-host) species from the genera Trypanosoma and Leishmania are subjects to thousands of studies aiming to help us understand various aspects of their molecular and cellular biology. Some of them had their genomes sequenced and now high quality reference genomes are available.
Nevertheless, it seems unlikely that genome analyses of just the dixenous species will reveal specific genetic elements responsible for successful parasite invasion. We would like to derive this information from genome sequencing and comparative analyses of monoxenous (single-host) species. For this purpose are sequencing, assembling and annotating genomes of selected monoxenous trypanosomatids belonging to phylogenetic clades, so far without a sequenced representative.
Euglena gracilis as a new model organism
Euglena gracilisis the evolutionarily closest free-living photosynthetic relative of the kinetoplastid parasites that cause serious diseases including African sleeping sickness, leishmaniasis and Chagas disease. Hence, this protist provides an evolutionary link to understand the emergence of several unique molecular processes in kinetoplastids. Moreover, Euglena spp. is also an ecologically significant, yet severely understudied protist. Despite the efforts of several laboratories, the Euglena genome project has not yet been assembled and the lack of tools for forward and reverse genetics makes Euglena refractory for molecular studies. It was shown recently that electroporation of dsRNA into its cells leads to specific degradation of the target sequence, although this process is only temporary, being lost after few generations. In our lab, we are going to analyze the genome project data with the emphasis on mitochondrial proteome, RNA editing and processing, and make a comparative analysis with the genomes of the parasitic groups within the phylum Euglenozoa. Moreover we will design and establish a transfection protocol of E. gracilis with the aim to achieve over-expression from a stably integrated construct. Provided this phase was successful, we will also generate cell line with T7-TR background, representing a tool for functional analysis of genes of interest using the RNAi approach.
Acyclic nucleaoside phosphonates as potent nhibitors of purine salvage pathway enzymes
The purine salvage pathway (PSP) in unicellular parasites complies with key requirements for essentiality, potential druggability, availability of in vitro assays, and availability of structural information of target enzymes. In contrast to their mammalian hosts, trypanosomatids (as well as malaria parasites) lost their ability to synthesize nucleoside monophosphates de novo and they rely entirely on the acquisition of purines from the host environment. Recently several enzymes of the PSP (i.e., GMP synthase, hypoxanthine-guanine-(xanthine) phosphoribosyltransferase HG(X)PRT) have been experimentally validated as potential therapeutic targets. It has also been shown that selected prodrugs of potent acyclic nucleoside phosphonates (ANPs), inhibitors of HGXPRT and HGPRT, block the growth of above-mentioned parasites.
The current study focused on Trypanosoma brucei (Tbr) purine salvage pathway (PSP). To complement our preliminary studies on key PSP enzymes, 6-oxopurine PRTs and their inhibitors (ANPs), we decided to add adenine PRT (APRT) to the studied portfolio of enzymes and study APRT side by side to 6-oxopurine PRTs.
Neglected role of parasites: does biomass of trematode cercariae matter in subarctic freshwater ecosystems?
Trematode cercariae (Digenea), essential components of aquatic food webs, can be released in thousands from molluscan hosts every day and generate a substantial biomass within ecosystems. The ecological role of cercariae and especially the strength of trophic interactions between cercariae and ambient communities remain to be tested in yet unexplored subarctic freshwater habitats. This project aims to fill this knowledge gap by addressing the biomass contribution of cercariae to energy flow in food webs. The novelty lies in linking experimental field and laboratory studies of a subarctic lake with a food-web approach to estimate cercarial production, biomass and survival of model trematode species in combination with the effects of predation by invertebrates and fish on cercarial populations. Identifying interactive effects of abiotic (i.e. temperature and light) and biotic factors in subarctic areas under unique climatic conditions allow a better understanding of the trematodes’ ecological relevance in food webs and develop future modelling approaches in context of climate change.
Czech Science Foundation (17-20936Y; P.I.: M. Soldánová; 2017–2019).
Epidemiology and immunology of microsporidiosis
The immune response mechanisms against the microsporidian Encephalitozoon cuniculi were studied. The role of specific anti-microsporidia antibodies in protection of infected mice was described based on results of experimental infections of immunocompetent mice compared with those of immunodeficient mice. Mice with disrupted IFN-? or IL-12 genes, and those with severe combined immunodeficiency, served as models of immunodeficient hosts. Adoptive transfer experiments of CD4+ and CD8+ T lymphocytes, in combination with antibodies applied in vivo, were used to examine the contribution of antibodies to protective immunity against microsporidians.
Free-living and captured mammals and birds are examined for microsporidia spores. New species of the genus Trachipleistophora has been described from muscles of Tenrec ecaudatus
Identification and analysis of repeats shaping lepidopteran genomes and sex chromosomes
Repetitive DNA is an inherent component of eukaryotic genomes. Tandem repeats are known to play a crucial role in maintaining chromosome integrity and function, as they occur in centromeres and telomeres. They are also the most rapidly evolving sequences in genomes. Mobile elements, the selfish DNA, shape the genome via multiple mechanisms which lead e.g. to change of gene transcription pattern or generation of structural chromosome aberrations. They often occur in compact genomic regions, i.e. heterochromatin. In moths and butterflies, usually, the only large heterochromatin block is the W chromosome, a sex chromosome unique to females, which is known to be gene-poor and rich in repeats. In this project, we study repetitive sequences that contribute to the W chromosome degeneration in representatives of various families, such as Pieridae, Geometridae, and Noctuidae, with the aim to detect possible inter- and intraspecific variability in both location and abundance of individual repeats on W and elsewhere in the genome and eventually identify mechanisms resulting in the diversification of the W and Z chromosomes. For this purpose, we carry out a comparative analysis of male and female genomes using bioinformatic tools such as RepeatExplorer and Tandem Repeats Finder. Selected repeats are then mapped by fluorescence in situ hybridization (FISH) to show their exact location on the chromosomes.
Figure: Analysis of repetitive DNA in Lepidoptera. a) Comparative genomic hybridization identifies W chromosome in Tischeria ekebladella (Tischeriidae). b) FISH mapping of a microsatellite in Lomaspilis marginata (Geometridae) by FISH. c) FISH mapping of a W-enriched satellite sequence in Pieris napi (Pieridae). d) Variability of presence and content of heterochromatin blocks in L. marginata revealed by FISH and DAPI staining. In b, c, and d, chromosomes are counterstained with DAPI (blue), hybridization signals of the probes are red. Bar = 10 um
[PI: M. Zrzavá]
Landscape ecology
To understand the drivers that affect insect communities at larger spatial scales and in long term, we study landscape changes using Geographic Information Systems (GIS). We characterize land cover types in past and in present, combine them with ecological background of studied organisms or mathematical models and relate these to current distribution of target species or target habitats. Our studies suggest that transition from traditional silvicultural practices to modern agriculture and forestry managements during last two centuries had an important negative impact on biodiversity of several groups of organisms.
Related maps:
Veteran trees and saproxylic insects in the floodplains of lower Morava and Dyje rivers: http://goo.gl/oeBgtn
Pollard willows in South Moravia: https://kfgg.maps.arcgis.com/apps/webappviewer/index.html?id=4d390794c9ec46b889269e744a8c5222
Related publications:
Miklin et al. 2018: Past levels of canopy closure affect the occurrence of veteran trees and flagship saproxylic beetles. Diversity and Distributions.
Anti-tick vaccines to prevent tick-borne diseases in Europe
7FP EU ANTIDotE (2014-2018)
The impacts of tropical forest degradation and fragmentation on ant-plant mutualisms
Project investigates how the mutualism between early succession Macaranga trees and their ant symbionts changes with logging and fragmentation of tropical forest, conversion to oil palm and experimental forest regeneration in Borneo. We will quantify network structure, and assess benefits for ants (food and living space) and trees (protection from herbivores). We will use field experiments to assess critical degrees of isolation from ant colonists for Macaranga and the potential for ant-assisted Macaranga to facilitate other trees.
Funding: 2016-2018: 16-09427S Czech Science Foundation (PI: T. Fayle)
Key studies:
Houadria M.Y.I., Klimes P., Fayle T.M., Gullan P.J. Host-plant dissections reveal contrasting distributions of Crematogaster ants and their symbionts in two myrmecophytic Macaranga species. Ecological Entomology 43: 601–611
Houadria M.Y.I. Feldhaar H., Fiala B., Lestina D., Chung A., Salleh A., Justin H., Kokorova P., Fayle T.M. (2020) Reduced benefits of ant occupation for ant-trees in oil palm compared with heavily logged forest. Symbiosis 81: 79-91.
Biodiversity in military training areas
Europe is scattered with hundreds of military areas, from huge training ranges to small garrison fields. Despite general view of such areas as deteriorated lands, they often host invaluable biological riches, not found in common farmland or woodland landscapes. Much of the standing biodiversity depends on small-scale disturbance succession dynamics typical for past military use. With changing military doctrine, these areas are progressively abandoned, and the fine-grained mosaics of various habitats are increasingly threatened either by succession, or by building development. In a cooperative project with several NGO, we carried out multi taxa comparison of 48 middle-sized abandoned military training areas, and our (not yet published) results advocate for a conservation use of these valuable sites.
Linking functional traits of three organism levels as driving mechanisms of ecosystem functions in the Arctic
Czech Science Foundation (CSF), team member, 2017-2019
There is an increasing evidence that functional traits of biota may serve as important indicators of ecosystem services. Although it is known that different organism levels interact in providing ecosystem services, there are so far only few studies linking functional traits of several trophic levels together. Here we proposed to interconnect functional traits of three organism levels plants, soil fauna and soil microorganisms - to ecosystem functions underlying ecosystem services in the Arctic terrestrial ecosystem, representing a less complex, model system. Several ecosystem functions were approached (C sequestration potential and soil stability, fertility and water retention) in a set of manipulative experiments. We expected that joining relevant functional traits across organism levels into "multitrophic" trait clusters will allow us to identify key traits underlying the ecosystem functions.
Human Antibodies to Tick-borne Flaviviruses
(Czech Science Foundation and Swiss National Science Foundation, international co-operation project Czech Republic- Switzerland, 2021-2023, P.I. Daniel Růžek)
Gene knockdown and functional research of Myxozoa
Despite the era of next-generation sequencing of Myxozoa, reverse genetics techniques are limited in myxozoan research. A significant step forward to explore the biological aspects of unprecedented Myxozoa embodies RNA interference (RNAi)-triggered gene knockdown. Therefore, we optimized and experimentally demonstrated a workflow for gene knockdown of unusual actins (Kyslík et al. 2024) related to the unique motility of a model system of carp infecting Sphaerospora molnari established in our laboratory from in vivo infected common carp. In this direction, we can use this invaluable research tool to explore previously unknown genes restricted to Myxozoa. We continue to investigate myxozoa-specific genes of unknown function using RNAi, which considerably supports the unraveling of many aspects of this mysterious group of parasites.
Combating the Poultry Red Mite (Dermanyssus gallinae): A Fight for Safer Eggs and Healthier Hens
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Diatomaceous earth: While popular on smaller farms, it can be labor-intensive and less effective against large infestations.
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Neurotoxic acaricides: These broad-spectrum pesticides offer strong control but carry a significant risk. Residues can contaminate eggs, leading to product withdrawals and even farm closures, as seen in recent fipronil cases.
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High-throughput testing platform: We've developed a sophisticated system for testing potential acaricides using ex vivo (outside the living host) blood feeding of mites. This allows us to efficiently evaluate a large number of compounds rapidly.
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Focus on safer options: Our goal is to develop acaricides that are effective against mites but pose minimal risk of contaminating eggs or harming humans.
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Joint project. We work closely with organic chemistry experts at Palacký University in Olomouc and industry partners.
The assembly of iron-sulfur clusters in Trypanosoma brucei
Trypanosoma brucei is characterized by a number of unique cellular features. Since methods of reverse genetics are available for this flagellate, it can now be considered a model protist. Iron-sulfur (Fe-S) clusters are ancient and ubiquitous cofactors of proteins that are involved in a variety of biological functions, including enzyme catalysis, electron transport and gene expression. Nevertheless, little is known about how Fe-S clusters are assembled in T. brucei. So far, by means of RNA interference, we have down-regulated several evolutionary highly conserved components of the pathway, such as cysteine desulfurase IscS, metallochaperone IscU, frataxin, ferredoxin, and IscA. With the exception of IscA, all are essential for the parasite and their down-regulation results in reduced activity of the marker Fe-S enzyme aconitase in both the mitochondrion and cytosol. Moreover, interfering with these genes also decreased the activity of succinate dehydrogenase and fumarase, affected membrane potential of the mitochondrion and general oxygen consumption. This supports the hypothesis that the mitochondrion plays a fundamental and evolutionary conserved role in cellular Fe-S cluster assembly throughout the eukaryotes. Interestingly, we have rescued the frataxin know-down in T. brucei with its homologue from the hydrogenosome of Trichomonas vaginalis containing the hydrogenosome-targeting signal peptide. Further analyses of this rescue and the various RNAi knock-downs are under way.
ECIP – European Centre of Ichthyoparasitology.
Fish parasitology belongs among very a few areas of bio-ecological research in the Czech Republic that actually play a leading role at the international level and have the highest international reputation. The proposed project to establish the European Centre of Ichthyoparasitology represents a follow-up of previous research, with several new innovations and main focus on complementarity, formation of young researchers and a more intensive mutual collaboration of all teams involved. The project is based on four moduls, each of them representing a different spectrum of methodological approaches to be applied in studies of seven basic groups of parasites (protists, myxozoans, monogeneans, endo helminths tapeworms, diplostomatid metacercariae and nematodes, and parasitic crustaceans) and their fish hosts. Multidisciplinarity and complementary of individual teams headed by a well balanced mixture of senior researchers renowned internationally, which will form the ECIP, is considered to be the strongest aspect of the proposed project.
Czech Science Foundation – centres of excellence (P505/12/G112; Co-P.I.: T. Scholz; P.I.: M. Gelnar, Masaryk University, Brno; 2012–2018).
Immune response in gastric mucosa during Cryptosporidium muris infection
Although scarcely any T-cells are presented in gastric mucosa of healthy rodent hosts, significantly elevated migration of T-lymphocytes (more than 10,000 fold), especially CD8+ T-lymphocytes, to the stomach mucosa occurred during primary infection and persisted for more than two months after its resolution. Most immunocompetent hosts self-cured during 35 days post infection (DPI). The ex vivo cultures of splenocytes revealed very low levels of IFN-? production during the course of the primary infection. These infected animals acquire a protective immunity against re-infection with same or another gastric Cryptosporidium. No cross immunity between gastric Cryptosporidium species of mammals and C. parvumhas been detected. The hosts with CD8+ or CD4+ T-cells deficiency suffered from chronic cryptosporidiosis; nevertheless, they were able to self-cure during 100 or 150 DPI, respectively.
Dung beetle ecology and conservation
Our group focuses on ecology and conservation of temperate and tropical dung-inhabiting communities. Such communities are species rich and serve as an excellent model for community ecology. They provide ecosystem services that are valuable for agricultural production. Regarding their ecology, we mainly focus on mechanisms responsible for maintaining high species richness (competition, trophic interactions) and community assembly (niche differentiation, habitat filtering). Regarding their conservation, we mainly focus on non-target effects of veterinary treatment of livestock, pasture management and effects of climate change on dung-inhabiting communities. We also co-operate with nature conservation authorities and NGOs.
Related publications:
Buse et al. 2015: Relative importance of pasture size and grazing continuity for the long-term conservation of European dung beetles. Biological Conservation.
Sladecek et al. 2017: Temporal Segregation between Dung-Inhabiting Beetle and Fly Species. PlosOne.
Impact of degradation of forests on ant/termite communities and their inter-species interactions
In this project we will assess the way that interactions between soil dwelling ants and termites change when tropical rainforest is logged, fragmented and converted into oil palm plantation. Interactions will be quantified using environmentally constrained null models of species cooccurrence, molecular identification of gut contents, and observations and experiments linking the soil biota to soil properties and nutrient redistribution rates. Using these data we will create whole-network models which will allow prediction of the stability of ecosystem diversity
and functioning under a range of species extinction scenarios.
Funding: 2014-2016: How do changes in species interaction networks affect ecosystem function when tropical forests are degraded? Czech Science Foundation (PI: T. Fayle)
Key studies:
Luke, S.H.; Fayle, T. M.; Eggleton, P.; Turner, E.C.; Davies, R.G. (2014) Biodiversity and Conservation 23 (11): 2817-2832.
Fayle T.M. et.al. (2015) PLoS ONE 10: e0122533.
Tuma J., Fleiss S., Eggleton P., Frouz J., Klimes P., Lewis O., Yusah K.M., Fayle T.M. 2019. Applied Soil Ecology 144: 123-133.
Organic matter decomposition and carbon sequestration on a natural gradient of labile carbon sources in coniferous temperate forest soils
Czech Science Foundation (CSF), principal investigator, 2017-2019
This project dealt with the effect of labile carbon (C) from various sources (litter, rhizodeposition, honeydew) on soil organic matter (SOM) decomposition and C sequestration in temperate coniferous forest soils, which are of global importance in terms of organic C storage. The proposed project mainly dealt with: (i) the rate of SOM decomposition and C sequestration on a natural gradient of labile C sources; (ii) potential increase in SOM decomposition and C sequestration with increased labile C input; (iii) effect of microbial and faunal community on labile C flux; and (iv) the role of respective labile C sources in C fluxes through soil. Field samplings and observations were combined with field and laboratory manipulation experiments, both followed by laboratory analyses.
Host-parasite interaction
We use transcriptomics and proteomics in combination with in vitro and in vivo experiments to better understand how myxozoan proliferative stages in carp blood are able to multiply rapidly in the host and to use resources effectively, while avoiding host immune defense mechanisms. Our model organism, S. molnari uses highly derived cytoplasmic actin to generate a completely novel type of cellular motility, which is of great importance for evading the attachment and lysis by host immune cells (Hartigan et al. 2016, Sci Rep 6:39093). Apart from this motility, S. molnari uses a wide repertoire of proteolytic enzymes and their inhibitors to survive and propagate in the host blood, some of which are expressed only during proliferation and are of particular importance to the early propagation of the parasite infection in fish (Hartigan et al. 2020, BMC Genomics 21:404; Bartošová-Sojková et al. 2021, Biology 10:110; Esterbauer et al. 2020, Microorganisms 8:1502). We are currently describing and characterizing some proteases and specific protease inhibitors biochemically and structurally. The main source of nutrients for the parasite's blood stages are red blood cells (Korytar et al. 2020, Parasite Immunol, 42:e12683). Their immunological responses and energy transfer/nutrition roles are under further investigation. In parallel, we explore the immunological reaction of carp to S. molnari which exists of several phases, an initial covert infection with minor proinflammatory characteristics which is skewed to a strong anti-inflammatory type once proliferative blood stages occur (Korytar et al. 2019, Parasit Vect 12:208). Additionally, we expanded the available knowledge of the kinetics of leukocytes subpopulations during the model infection and evaluated their proliferative capacity in main lymphoid organs. The proliferation led to a substantial increase in the number of circulating B lymphocytes producing S. molnari specific antibodies. These antibodies, exerting potent killing capacity in vitro, do not prevent the proliferation of the parasite in vivo, indicating a possible antibody evasion strategy employed by the parasite. Current work focuses on the characterization of changes in the antigenic composition during the parasite's life cycle and its impact on B cell responses.
Mitochondrial peptidases in T. brucei
Most mitochondrial proteins are nuclear-encoded and translocated into this organelle. Some of the pathways of protein translocation into the mitochondrion recognize a pre-sequence in the N-terminus of the nascent protein for this process to take place. Once in the mitochondrial matrix, the pre-sequence is cleaved off by mitochondrial processing peptidases, which may perform one, two or even three cuts in one single substrate. We aim to characterize these proteins in the mitochondrion of T. brucei and determine the extent of their involvement in the stabilization of the mitochondrial protein pool.
Other evolutionarily conserved proteases with known moonlighting functions have evolved new roles in the mitochondrion of T. brucei. The presence of certain Leucine Amino Peptidases (LAP) known to be involved in n-terminal cleavage of amino acids as well as glutathione metabolism are in T. brucei distributed in diverse cellular compartments involved in tasks related to cytokinesis and mitochondrial stability.
Functional Analysis of Babesia Calcium-Dependent Protein Kinases
Project:GAČR: 21-11299S
EN: This research is aimed at tick-borne apicomplexan parasites of the genus Babesia, which infects a range of animals and humans. We focus on the parasite's ability to invade host erythrocytes, a trait it shares with its relative Plasmodium, the cause of malaria. Our team is employing cutting-edge transgenic techniques to conduct a thorough examination of previously unknown calcium-dependent protein kinases (CDPKs) in Babesia divergens. By exploring the role of these enzymes in key biological processes, we aim to understand their function and potential as drug targets. This includes using Bumped Kinase Inhibitors (BKIs) to selectively inhibit these enzymes and assessing their effectiveness in combating the parasite.
Researc Articles:
PMID: 36014069
PMID: 38156314
PMID: 38104025
PMID: 38287902
Phylogeography and population biology of Melanesian ants
This project represents a comprehensive study of the ecology and evolution of tropical ants at the community, species and population levels. It is based on unique data set of samples collected from 17 sites in New Guinea and northern Australia. The study examines species distributional data combined with their population and species phylogenetic relationships across a large regional spatial scale. We used several different standartized collection methods (e.g. Wincler extractors, hand colecting, pitfall-traps, baits, searching of fallen trees) resulting to a broad focus on cryptic, terrestrial and arboreal ant species.
Funding: 2012-2015 Ecological and evolutionary determinants of ant distributions in tropical ecosystems. Czech Science Foundation (PI: M. Janda)
Key publications:
Janda M., Matos Maravi P., Borovanska M., Zima J. jr., Youngerman E., Pierce N., (2016) Phylogeny and population genetic structure of the ant genus Acropyga (Hymenoptera: Formicidae) in New Guinea. Invertebrate Systematics 30: 28-40.
Matos Maraví P.F., Clouse R., Sarnat E., Economo E., LaPolla J.S., Borovanská M., Rabeling C., Czekanski-Moir J., Latumahina F., Wilson E., Janda M.(2018) An ant genus-group (Prenolepis) illuminates the biogeography and drivers of insect diversification in the Indo-Pacific. Molecular Phylogenetics and Evolution 123: 16-25.
Matos‐Maraví P.F., Matzke N.J., Larabee F.J., Clouse R.M., Wheeler W.C., Sorger M.D., Suarez A.V., Janda M. (2018) Taxon Cycle predictions supported by model‐based inference in Indo‐Pacific trap‐jaw ants (Hymenoptera: Formicidae: Odontomachus). Molecular Ecology 27: 4090-4107. (research article)
PARASITIC PROTISTS
Apart from our main focus on myxozoans, we investigate a wide diversity of protists in aquatic environments and hosts, studying their distribution, host-parasite interaction, pathology, ecology as well as functional and evolutionary aspects. Here’s some of our recent and ongoing research in our on lab and as collaborators:
RNA editing, mitochondrial biogenesis and dynamics
Our laboratory is interested in various aspects of trypanosome mitochondrial biology, such as organellar gene expression. In this respect, we have been focused on the unique process of kinetoplastid U-insertion/deletion RNA editing, a vital process that is required for decrypting mitochondrial RNAs into bona fide templates for translation. These RNAs mainly encode subunits of the respiratory chain, which are vital for mitochondrial physiology. The membrane potential generated from this process is needed for various other pathways underlying mitochondrial biogenesis, such as protein import and the maintenance of mitochondrial volume. To this end, we have begun to investigate factors that are involved in shaping the organelle.
Mitochondria are very dynamic organelles which are constantly reshaped by fission and fusion processes. T. brucei parasites have a single continuous mitochondrion throughout their life cycle which needs to divide only once during the cell cycle just prior to cytokinesis. The only protein identified to date that was shown to play a role in trypanosome mitochondrial division is a dynamin-like protein (DLP). We are interested in identifying other proteins involved in mitochondrial dynamics such as potential adaptors that interact with DLP in both bloodstream and procyclic life stages.
Master proteases driving the apical complex of Babesia parasites
GAČR: GA23-07850S
This project focuses on specific proteolytic enzymes appearing on the top of a proteolytic cascade directly driving the function of apical complex during host cell egress and invasion by apicomplexan parasites. An in silico comparative analysis of Babesia omics datasets utilizing Toxoplasma and Plasmodium queries determined candidate proteolytic enzymes in Babesia divergens that will be further functionally and biochemically characterized to confirm their essential role for the parasite and their potential druggability with low molecular weight inhibitors. Main focus is dedicated to two B. divergens aspartyl protease homologues of Plasmodium falciparum plasmepsins IX/X and Toxoplasma gondii TgASP3 tagged BdASP3a/b as potential master drivers of the apical complex and molecular events associated with egress and invasion of host red blood cells.
Research Articles: PMID: 37271664
Taxonomy of new species of social insects
We also collaborate and share our material with international museums and taxonomists for identifications and possible descriptions of news species of social insects, notably ants and their nest symbionts.
Examples of collaborative institutions are: Museum of Comparative Zoology Harvard, Australian National Collections, National Agriculture Reasearch Institute of Papua New Guinea, Natural History Museum London.
Just from forests of New Guinea we have described 5 new species of ants and one new genus of symbiotic beetle.
Key papers:
Klimeš P, McArthur A (2014) Diversity and ecology of arboricolous ant communities of Camponotus (Hymenoptera: Formicidae) in a New Guinea rainforest with descriptions of four new species. Myrmecological News 20: 141-158.
Hlaváč P., Janda M., (2009) New genus of Lomechusini (Coleoptera: Staphylinidae, Aleocharinae) from Papua New Guinea associated with Leptogenys Roger. Zootaxa 2062: 57-64.
Research into free-living and amphizoic amoebae
A large-scale phylogenomic study focussed on free-living testate amoebe because they have, due to their shells, a fossile record and can provide invaluable information on early eukaryote evolution. Based on 324 genes and 19 testate amoebae it was shown that the major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Proterozoic (Lahr et al. unpublished). Applied research encompases studies on the pathological agent involved in outbreaks of amoebic gill disease (AGD) in Atlantic salmon in Northern Europe (Paramoeba perurans) and we are testing a variety of substances for their efficacy against P. perurans and their suitability as in-feed treatments against AGD. Most of this research is sponsored by the R&D department of Skretting Aquaculture Research Centre. We also screen for of a variety of pathogenic amoebae in water sources impacted by human actions, using molecular methods, and we have a unique, comprehensive culture collection of amphizoic amoebae from different aquatic habitats and hosts, with hundreds of different strains.
Define Biology of Babesia – Hemoglobin as a Source of Nutrients for Intracellular Parasite Development and Disease Progression
Project: MSCA4Ukraine-Viktoriya Levytska
A deeper understanding of uptake and utilization of hemoglobin may result in the identificatin of numerous potential vulnerable targets ultimately leading to the rational design of alternative anti-Babesia strategies and hereby become a valuable basis for translational research by human and/or veterinary pharma companies.
Functional analysis of RNA editing in Trypanosoma brucei
We have generated knock-down cell lines of T. brucei procyclics, in which RNA binding proteins MRP1 and MRP2 are down-regulated by RNA interference. We have shown that these proteins exist in a complex composed of two MRP1 and MRP2 molecules each, which is involved in RNA editing and stabilization of mitochondrial transcripts. In a collaborative effort, we would like not only to decipher the 3D structure of this complex, but also to understand how RNA molecules are bound to it. Moreover, we are using the newly developed TAP-purification method to detect binding partners of the MRP proteins and another RNA-binding protein, TbRGG1. Furthermore, we will dissect the function of individual MRP protein domains.
New Guinea ants - photos and database
The website dedicated to providing information about the systematics and ecology of the New Guinean ant fauna is available on www.newguineants.org. Our long-term aim is to facilitate access to photographs of specimens, their nests and habitats and provide resources for better knowledge of Melanesian ants with main focus on New Guinea island.
Running research projects
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Hidden in the honeycomb: Microsporidian and trypanosomatid parasites in bees identified by metabarcoding approach Czech Science Foundation (25-16047S, PI: P. Sojková. 2025-2027).
- Harnessing the Win-Win potential: Enhancing sustainability and disease control in aquaculture by using black soldier fly larvae fed on agricultural waste. Ministry of Education, Youth and Sport of the Czech Republic, program Inter-Excellence, subprogram Inter-Action. (LUAIZ24009, 2024-2027, PI: S. Nayak)
- Food or foe: Interaction of myxozoans with red blood cells. Czech Science Foundation and Austrian Science Fund. (24-13238L, PI: P. Sojková. 2024-2027).
- Unveiling the impact of human activities on the distribution of parasites in aquatic ecosystems using metagenomic analysis. Ministry of Education, Youth and Sport of the Czech Republic, program Inter-Excellence, subprogram Inter-Action. (LUAUS24281, 2024-2027, PI: I. Fiala)
- Biodiversity Shifts in Myxozoan and Microsporidian Parasites: The Role of Human Activity and Sewage Treatment Plant in Živný Stream. Grant Agency of the University of South Bohemia. (PI: M. Bürgerová)
- Living jewels under the water surface of Šumava. Interreg Bavorsko – Česko BYCZ01-020. https://www.fishjewels.cz/ (Inst. of Parasitology Co-PI: I.Fiala)
- Myxozoan cystatins and fish host cathepsins: Revealing potential crosstalk during infection. Czech Science Foundation (21-16565S, PI: P. Sojková. 2021-2023).
- Complex characterisation of myxozoan mitochondria: Genome, proteome and ultrastructure approach. Czech Science Foundation. (21-29370S, PI: I. Fiala, 2021-2023)
Project of the Czech Technology Agency in the TREND Programme: FW10010308 Formulation of an acaricide for the elimination of the important poultry parasite Dermanyssus gallinae
Principal investigator: Tekro, spol. s r.o., Ing. Martin Jeřábek, Ph.D.
For Biology Centre CAS: Mgr. Jan Perner, Ph.D.
Objective of the project: The development of effective preparation for extermination of red mite in laying hens based on nitisinone derivatives.The positive aspect of the new product is the different mechanism of action compared to the commonly used fluralaner product, which prevents possible cross-resistance.The intention is to increase bioavailability,which can reduce the total amount use of active substances while the same efficacy is maintained,which has positive effects on the environment and its lower burden,lower toxicity to hens and lower potential risk for humans.Higher bioavailability is achieved by using a suitable nitisinon derivative and its sustained release in laying hens organism.This technology is unique and innovative in the production of drugs.These facts contribute to greater competitiveness.
Project results: Prototype (unctional formulation of a veterinary drug for the elimination of red mite) and Validated technology (The manufacturing process of a veterinary medicinal product).
This project is co-financed through the Czech Technology Agency under the National Recovery Plan from the European Recovery and Resilience Facility.
Evolution and biodiversity of Kinetoplastida
Kinetoplastida are omnipresent and serious parasites of animals and plants. Using conserved rRNA and protein-coding gene sequences, we are mapping biodiversity of species infecting insects and vertebrates. Moreover, we would like to shed light on the evolution of hallmark features of the kinetoplastid flagellates, such as the extremely complex mitochondrial (= kinetoplast) genome and RNA editing. Insect trypanosomatids from North, Central, and South America that are collected will be used not only for phylogenetic analyses, but also to study components of their respiratory complexes. We would also like to understand the process of dyskinetoplastidy (loss of kinetoplast DNA), in particular its extent in species pathogenic for horses (Trypanosoma equiperdum) and possibly also for humans (Trypanosoma evansi).
Analysis of dyskinetoplastic trypanosomes
Trypanosoma brucei is a kinetoplastid flagellate, the agent of human sleeping sickness and ruminant nagana in Africa. Kinetoplastid flagellates contain their eponym kinetoplast DNA (kDNA), consisting of two types of interlocked circular DNA molecules: scores of maxicircles (each ~23 kb) and thousands of minicircles (~1.0 kb). Maxicircles have typical mt genes, most of which are translatable only after RNA editing. Minicircles encode guide (g) RNAs, required for decrypting the maxicircle transcripts. The life cycle of T. brucei involves a bloodstream stage (BS) in vertebrates and a procyclic stage (PS) in the tsetse fly vector. Partial (dyskinetoplastidy, Dk) or total loss (akinetoplastidy, Ak) of kDNA locks the trypanosome in the BS form. Transmission between vertebrates becomes mechanical without PS and tsetse mediation, allowing the parasite to spread outside the African tsetse belt. Trypanosoma equiperdum and Trypanosoma evansi are agents of dourine and surra, diseases of horses, camels, and water buffalos. We have characterized representative strains of T. equiperdum and T. evansi by numerous molecular and classical parasitological approaches. We show that both species are actually strains of T. brucei, which lost part (Dk) or all (Ak) of their kDNA. These trypanosomes are not monophyletic clades and do not qualify for species status. They should be considered two subspecies, respectively T. brucei equiperdum and T. brucei evansi, which spontaneously arose recently. Dk/Ak trypanosomes may potentially emerge repeatedly from T. brucei.