Laboratory of Environmental genomics

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.

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.

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).

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.

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

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

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.

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).

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.

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).

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

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.

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). 

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. 

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

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)

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.

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.

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.

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.

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).

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.

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)

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)

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)

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.

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.

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).

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)

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:

• 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.).

• 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.

Pathogesis and therapy of emerging viral diseases

(The National Institute for Virology nad Bacteriology, 2022-2025, coordinator for BC: Daniel Růžek)

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:

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.

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.

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.

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.

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]

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. 

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.

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.

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.

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).

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

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.

Molecular pathogenesis of alimentary infection by tick-borne encephalitis virus

(Czech Science Foundation, 2023-2025, Co-P.I. Jiří Salát)

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.

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.

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.

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).

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). 

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)

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.

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]

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.

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

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.

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.

Evolution of symbiotic bacteria associated with arthropods

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.

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.

Nuclear export of tRNAs in trypanosomes

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.  

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]

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 

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.

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.

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:

• 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

• 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

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).

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

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.

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).

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]

Anti-tick vaccines to prevent tick-borne diseases in Europe

7FP EU ANTIDotE (2014-2018)

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.

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)

Combating the Poultry Red Mite (Dermanyssus gallinae): A Fight for Safer Eggs and Healthier Hens

• Diatomaceous earth: While popular on smaller farms, it can be labor-intensive and less effective against large infestations.
• 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.

• 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.
• 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.
• Joint project. We work closely with organic chemistry experts at Palacký University in Olomouc and industry partners.

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).

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.

Ekology of woodland butterflies

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. 

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

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:                                                                      

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

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.                                                                    

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.

Running research projects

• 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)

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).