Research projects

Ongoing research projects

Ongoing research projects

The laboratory staff is engaged in three projects of the Jan Amos Komenský Operational Programme (Inter-micro, Photomachines, Micro-biotech), the MSCA-CZ project (Marie Skłodowska-Curie Actions, Molecular basis for determining the competence of ticks in the transmission of pathogens), and other projects. The Ministry of Education, Youth and Sports is engaged in research on the secondary metabolism of intracellular pathogens and the development and evaluation of a web-based screening tool for assessing diet quality in vegans. The Health Research Grant Agency is investigating invasive aspergillosis in a prospective study, while the Czech Grant Agency is examining the spatial metabolomics of central nervous system infections.

Secondary metabolism of intracellular pathogens

Vladimír Havlíček

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. LUAUS24214 (2024-2028)

We will explore the metabolism of clinically relevant intracellular pathogens within host cells in collaboration with Stanford University. The research will thoroughly investigate the secondary metabolism of the endemic fungus Coccidioides immitis, as well as study mycoviruses and bacterial endosymbionts in fungi, bacteriophages in bacteria, and Mycobacterium tuberculosis in mammalian cells.

A prospective study on invasive pulmonary aspergilosis

Vladimír Havlíček

Supported by Czech Health Research Council, grant No. NU23-05-00095 (2023-2026)

The aims of the project are: 1. In a prospective format, to generate critical diagnostic parameters (sensitivity, specificity, negative and positive predictive values) in a larger cohort of patients with invasive pulmonary aspergilosis. 2. To provide a fair kinetic comparison between standard PCR, routine mycological serology, microscopy, microbiology, imaging data, and our next-generation PTX3/siderophore panel. 3. To develop an affinity-based TafC preconcentration workflow for the enrichment of siderophores in human bodily fluids.
INTER-MICRO: Talking microbes - understanding microbial interactions within One Health framework

Jan Jansa/Andrea Palyzová

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/22_008/0004597 (2024-2028)
INTER-MICRO advances the understanding of communication within microbial communities and between microbes and their hosts. The project will utilize knowledge from biology and chemistry, as well as different research areas within each discipline. These areas include general microbiology, microbial physiology and ecology, immunology, biochemistry, molecular biology, organic chemistry, and chemical engineering. The project will be supported by advanced biochemical, microscopic, molecular biological, and bioinformatics expertise and infrastructures. Our MS and microbiology groups contribute to this project using mass spectrometry and our Infection metallomics strategies.
Molecular fundamentals driving tick competence in pathogen transmission

Lenka Minichová

Supported by the Ministry of Education, Youth and Sports of the Czech Republic (Marie Sklodowska-Curie Action-CZ, 2024-2026)
Climate change is already affecting vector-borne disease transmission and spreading to new areas. Whereas they are responsible for more than 17% of all infectious diseases (causing more than 700 000 deaths annually) vector control and preventing the outbreaks become one of the WHO’s priorities. This project will elucidate the vector competence for pathogen transfer and describe the molecular and functional interface between the pathogenic bacteria (Rickettsia spp. and Coxiella burnetii) and their common tick vectors in Europe (Dermacentor marginatus and Ixodes ricinus). Both pathogens can cause severe illnesses in humans or economic losses in ruminants (goats, sheep, cows), respectively. Pathogenic and immune pathways together with mechanisms of pathogen survival within the vector and host were characterized, but only a few studies were focused on the complex pathogen-vector interactions during feeding. To expand the borders of our knowledge, I will apply an interdisciplinary approach and state-of-the-art imaging techniques to describe how the tick immune system may control the preservation of pathogens and their transmission. My objective is (i) to develop new strategies for visualization and quantitation of tick-borne pathogens using state-of-art imaging techniques. This will lead me to (ii) identification of biomarkers (specific metabolites and proteins) important for pathogen transmission, which will be annotated or determined de novo. Finally, I will (iii) use identified tick-specific compounds modulated by bacterial factors as targets for defining effective antimicrobial therapy and development of protective antigens capable of blocking pathogens’ transmission.
Microorganisms in ecological restoration - bacteria as cell factories for controlled bioremediation of ecosystems

Marek Kuzma

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/23_020/0008502 (2025-2028)
A large Jan Amos Komensky project on new bioremediation strategies involves the Institute of Microbiology (IMIC), Charles University, Envisan, and Deconta. The project will fund the upgrade of NMR spectrometers installed at IMIC.
Photomachines: Photosynthetic cell redesign for high yields of therapeutic peptides

Roman Sobotka/Marek Kuzma

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/22_008/0004624 (2024-2028)
The project will successfully design and develop photomachines, a new type of photosynthetic production cells that will achieve high productivity. The project is divided into two Research Objectives and 13 specific tasks that synergistically convert a cyanobacterial cell into a ‘bio-factory’, called Syn2Cell. A key feature of this system is the strict separation of the growth and production phases. Our NMR group contributes to this project through the use of NMR spectroscopy.
Development and evaluation of a web-based diet quality screener for vegans

Marek Kuzma

Supported by Ministry of Education, Youth and Sports of the Czech Republic, grant No. 8F22003 (2022-2025)

The overall aim of the project VEGANScreener is the prevention and early detection of nutritional deficiencies in the diet of European individuals who have adopted mostly plant-based dietary patterns and particularly in the vegan population. To achieve this goal, we will develop and validate a standardized and brief web- and app-based dietary screening tool to assess and monitor dietary intake among vegans, and we will take first steps towards end-user application. A particular challenge for conducting dietary studies in vegans is the accurate and comprehensive assessment of the consumption of vegan and vegetarian foods, such as plant-based milks, meat alternatives, algae, and calcium-rich mineral water and meat alternatives. These foods are not sufficiently inquired about in FFQs of existing cohort studies, such as the NutriNet Sante, Nurses’ Health Study and UK Biobank. Therefore, extracting vegans from those cohorts would not allow for assessing vegan dietary patterns of today. In order to reach the research aims of the current proposal pertaining to the validation of a novel vegan diet screener, 400 vegans across four European countries (Belgium Czech Republic, Germany, Spain) will be newly recruited. The number of subjects needed for the validation of a diet screener is based on our previous experience. We will, however, make use of existing data already collected among vegans, such as the cohorts available in the Czech Republic and Germany whenever possible, i.e. for developing and pre-testing the diet quality metrics. Further, novel biomarker approaches including metabolomics will be applied to work towards identifying vegan subtypes. Lastly, in a first step towards broader end-user acceptability, digital applications geared toward health care providers (informational and educational website) and the enduser vegans (app to self-assess vegan’s diet quality), will be developed and piloted for acceptability and use.

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