Environmental Health Sciences

Aims: The aim of the thesis is to build a framework for estimating effects of xenobiotics on human microbiome metabolic pathways.

Background and methods: Food with its variety of dietary compounds, environmental chemicals, pollutants, as well as medications can be considered as xenobiotics to the human microbiome. In homeostasis (the healthy state that is maintained by the constant adjustment of biochemical and physiological pathways), human microbiome provides an extra set of biochemical reactions. The intrusion of xenobiotics has the potential to introduce a departure from homeostasis in many ways seen from the perspective of human microbiome, but both human cells and microbial communities living in their surroundings have to cope with these perturbations: pollutants can trigger latent enzymatic activities changing the functional potential of these microbial consortia; other drug metabolites can block important enzymes or can be biotransformed making antibiotics or other medical interventions useless or ineffective. Such perturbations (blocks and diversions of normal enzymatic activities) can be modeled and explored in the context of metabolic network models. Computational System Biology approaches can model and explore consequences of changes in the structure of networks simulated by random or target attack to nodes/metabolites in the metabolic network of the microbiome of interest. The assembled metabolic network model for the community understudy will be dynamically “updated” based on selected computational approaches aimed at predicting latent enzymatic activities (edge insertion update), enzymatic inhibition (edge deletion update), or changes in kinetics (edge weight update).

Supervisor

Mgr. Eva Budinská, Ph.D.

Bioluminescence is a fascinating phenomenon involving the emission of visible light by a living creature. There is an enormous interest in harnessing bioluminescence to design ultrasensitive optical bioassays but also zero-electricity lighting devices. Bioluminescent organisms generate light via the oxidation of a substrate (a luciferin), which is catalysed by a class of enzymes called luciferases. Bioluminescent apparatuses of diverse origins are being identified continually but our precise understanding in molecular terms of their structural complexity and inner workings remains sparse. In this project, we will structurally and biochemically characterise newly identified bioluminescent systems, for example the luminous brittle star Amphiura filiformis, using an integrative multi-method biology approach. Moreover, we will explore ways for exploiting the gained molecular knowledge for biotechnology and biomedicine, applying rational protein design approaches.
Methods: Bioinformatics, molecular biology, structural biology (X-ray crystallography), protein engineering, genome mining approaches, in-lab protein evolution, protein biochemistry and biophysics, molecular cloning and gene assembly, kinetic methods, high-throughput screening technologies, luminescent assays, cell-based assays
Lab website: https://loschmidt.chemi.muni.cz/

Supervisor

Ing. RNDr. Martin Marek, Ph.D., MBA

The ability to adapt to changing environments becomes increasingly critical with humanity’s impact on the planet. Natural selection followed by allele fixation acting on standing genetic variation and mutation accumulation within gene pools of current species acts slowly compared to rapid Anthropocene environmental changes. An alternative evolutionary mechanism is to capture pre-adapted genes from other organisms. Gene capture facilitates new resource acquisition, giving organisms an evolutionary advantage in timescales relevant to the rate of human-induced environmental modifications. The student will investigate horizontal gene transfer between recognised taxa and introgression from sister taxa using phylogenetics-based and population genetics-based algorithms, aiming to model reticulate evolution in wildlife and domesticated species. The goal of the project is to find genomic regions where convergent evolution and introgression promote species survival in human-influenced landscapes. [Please note: before initiating formal application to PhD studies at MUNI, potential candidates are requested to contact Dr. Martinkova for informal consultations]

Supervisor

doc. Mgr. Natália Martínková, Ph.D.

The recent advancements of Machine Learning (ML) techniques, coupled with growing protein data, provide promising directions for protein engineering. There are three types of protein data with an excellent ML potential: (i) in silico simulations, (ii) experimental measurements, and (iii) databases of protein sequences and structures. While ML has already leveraged some data from all the three sources in various applications in protein engineering, the field has only recently emerged, and much data remain unexplored. This project aims to explore the potential of machine learning methods in collecting protein data, reducing its dimensionality, performing data analysis, prediction, and optimization, to produce designs of improved proteins. The impact will primarily be (i) the new knowledge of the underlying mechanisms, (ii) promising protein variants, and (iii) user-friendly software tools that will provide access to the developed algorithms to the broader community of protein engineers.

Supervisor

Stanislav Mazurenko, PhD

Cílem práce bude studium enzymů pomocí výpočetních metod molekulového modelování a bioinformatiky. Výstupem analýz budou nejen nové poznatky v enzymologii, ale také varianty enzymů vytvořené metodami proteinového inženýrství, které budou mít potenciál v biotechnologických či biomedicínských aplikacích. Analýzy i design nových variant se zaměří na vylepšování stability molekul, které budou studovány metodami jako je Rosetta, FoldX nebo FireProt. Dále bude studována a optimalizována aktivita, specificita a selektivita enzymů metodami molekulového dokování, molekulové dynamiky, kvantová chemie a dalších. Poznatky ze studia enzymů budou také využity pro zlepšování softwarových nástrojů k analýze a designu proteinů, které tým v Loschmidtových laboratořích dlouhodobě vyvíjí.

The aim of this thesis will be to study enzymes by in silico approaches of molecular modeling and bioinformatics. The outcomes of the project will be used both in understanding the basics of enzymology and also to design enzyme variants by methods of protein engineering which can be applicable in biotechnology or biomedicine. The analysis and design of new enzyme variants will focus on improving the protein stability by methods like Rosetta, FoldX, or FireProt. Morover, other enzyme properties like activity, selectivity, or specificity will be analysed and optimized by molecular docking, molecular dynamics, or quantum chemistry calculations. The knowledge obtained during the analysis and design of enzymes will be utilized to improve functionality of software tools for protein engineering which are developed in Loschmidt laboratories.

Supervisor

doc. Mgr. David Bednář, Ph.D.

OBJECTIVES: The research aims to explore mechanisms (molecular toxicology, biomarkers of effects, toxicogenomic responses) triggered in humans and natural biota by organic pollutants, their metabolites and mixtures. The outcomes contribute to protection of the environment and health by providing scientific evidence and support to pragmatic risk assessment and management of chemicals.

FOCUS: Doctoral research projects focus on the effects of chemical groups that are broadly used in practice but their (eco)toxicological characterization is poor such as novel types of flame retardants, pharmaceuticals, pesticides and other potential endocrine-disrupters. Students benefit from outstanding research facilities of RECETOX that include high-end analytical instrumentations, molecular toxicology laboratories, alternative toxicological models - aquatic invertebrates and zebrafish.

EXAMPLES of potential student doctoral projects:
* Development of quantitative Adverse Outcome Pathways (AOPs) for liver toxicity and obesogenicity
* AOP networks beyond the male reproductive disorders
* In vitro toxicological investigations of novel flame retardants
* Molecular and biochemical effect biomarkers of low-dose mixture exposures in human cohort samples
* Automated text-mining approaches integrating toxicological data to toxicological knowledge

MORE INFORMATION: www.recetox.muni.cz

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Ludek Blaha (blaha@sci.muni.cz) for informal discussion.

Supervisor

prof. RNDr. Luděk Bláha, Ph.D.

Práce se bude zaměřovat na nové přístupy hodnocení vlivu vybraných faktorů exposomu na biomarkery efektu a možná zdravotní rizika v lidské populaci. Hodnoceny budou například vybrané skupiny chemických látek a stresorů, které byly prioritizovány v rámci mezinárodního projektu HBM4EU a PARC. Důraz bude kladen také na statistické metody hodnocení. Do analýz budou zahrnuta jak data o externí a interní expozici chemickým směsím, tak i výsledky analýz biomarkerů efektu. Metody budou aplikovány na reálná data získaná z kohortových studií (například CELSPAC–FIREexpo, CELSPAC-SPECIMEn, CELSPAC-YA, atd.), ale také i z populačních dat. Detaily o tomto Ph.D. výzkumném zaměření budou sděleny při osobní konzultaci - doc. RNDr. Pavel Čupr, Ph.D. (pavel.cupr@recetox.muni.cz). Zaměření odborné skupiny je popsáno zde - WEB EHRA: https://www.recetox.muni.cz/hear Před výběrem výzkumného zaměření mne prosím kontaktujte: pavel.cupr@recetox.muni.cz.

The work will be focused on new approaches for evaluating the influence of selected exposome factors on biomarkers of effect and possible health risks in the human population. For example, selected groups of chemical substances and stressors that were prioritized within the international project HBM4EU and PARC will be evaluated. Emphasis will also be placed on statistical evaluation methods (R-scripts). The analyzes will include data on external and internal exposure to chemical mixtures, as well as the results of analyzes of selected effect biomarkers. The methods will be applied to real data obtained from cohort studies (for example: CELSPAC–FIREexpo, CELSPAC-SPECIMEn, CELSPAC-YA, etc.), but potential also from population data. Details about this Ph.D. research focus will be communicated during a personal consultation - doc. RNDr. Pavel Čupr, Ph.D. (pavel.cupr@recetox.muni.cz). The focus of the expert group is described here - WEB EHRA: https://www.recetox.muni.cz/hear Before choosing a research focus, please contact me: pavel.cupr@recetox.muni.cz.

Supervisor

doc. RNDr. Pavel Čupr, Ph.D.

OBJECTIVES: Access to water of sufficient quality is a major societal issue, and the present research aims to investigate processes during final purification of waste waters suitable for recycling and re-use for different purposes. Currently, new combinations of technologies for final purification of recycled water are being introduced at waste water treatment plants, WWTPs. These include, e.g., UV/UVLED disinfection, ozonization, cavitation/plasma, use of reactive nanomaterials etc. However, the full impacts on the final water quality have not been fully elucidated.

FOCUS: The doctoral research, which is a part of multi-partner applied projects supported by TAČR, will combine chemical analytical tools (including LC-MS/MS) together with bioanalytical approaches (cell-based in vitro assays and ecotoxicological models) to investigate performance of various WWTP technologies focusing on micropollutants, endocrine disruptive compounds and their transformation products and metabolites. The results will be combined with other water quality parameters such as microbiota, antibiotic resistence, etc., to fully characterize, improve and automatize (digital twin models) processes for recycling of waste waters.

ADDITIONAL INFORMATION: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Ludek Blaha (blaha@sci.muni.cz) for informal discussion.

Supervisor

prof. RNDr. Luděk Bláha, Ph.D.

Exposure to chemical substances in the environment can significantly contribute to the risk of developing cancer. The identification of substances with carcinogenic potential is, therefore, a key element in protecting human health. Non-genotoxic carcinogens (NGTxCs), unlike genotoxic carcinogens, do not damage DNA but instead promote tumor growth by affecting signaling and regulatory pathways, leading to the disruption of tissue homeostasis and the manifestation of cancer hallmarks.
The thesis will focus on a crucial homeostatic mechanism, gap junctional intercellular communication (GJIC), and how NGTxC-induced disruption of GJIC is linked to other cancer-related phenotypic changes, such as dysregulated proliferation, programmed cell death, migration, or epigenetic modifications. These relationships will be explored in both 2D and 3D in vitro rodent and human cell cultures, utilizing cellomics and transcriptomics approaches. The aim is to characterize mechanistic links between dysregulated GJIC and downstream alterations in cellular behavior, and evaluate their predictive capacity for the in vitro identification of NGTxCs with specific modes of action.
As a PhD researcher, you will have an exciting opportunity to:

• Employ advanced in vitro models of mammalian and human cells, including stem-cell-based cultures and 3D culture techniques
• Investigate the effects of chemicals of interest on a variety of cancer-relevant endpoints using real-time cell analysis, automated microscopy and cellomics techniques
• Unravel the mechanisms of non-genotoxic carcinogens using molecular biology and transcriptomics methods, and the role of environmental exposures to NGTxCs in cancer development
• Contribute to the development of in vitro assays and New Approach Methodologies (NAMs) suitable for hazard identification and assessment of non-genotoxic carcinogens for regulatory purposes, in connection with international projects and initiatives

Supervisor

doc. RNDr. Pavel Babica, Ph.D.

Compounds of emerging concern (CECs), such as aromatic amines, pharmaceuticals, personal care products or currently used pesticides are recognized as new classes of water contaminants due to their proven or potential adverse effects on aquatic ecosystems and human health.

The objective of the dissertation is to elucidate the pathway of selected CECs from different emission sources in urban wastewaters until their discharge to receiving waters. This will be achieved by a combination of various approaches to environmental sampling and chemical analysis of urban wastewaters.

Sewage wastewater will be collected from a sewer system channel before mixing with other wastewater influents. Additionally, samples from the wastewater treatment plant (WWTP) influent, effluent and downstream of the receiving river will be collected in accordance with the hydraulic retention time of the WWTP, in order to collect the same lot of WW along the way of treatment. The samples will be collected with passive samplers or other suitable techniques. The samples will be analyzed by a high-resolution mass spectrometric methods and data subjected to statistical analysis to understand source-related patterns i.e. peaks representing a certain emission source of CECs such as CESs peaks occurring only in extracts related to a certain type of an source (by cluster analysis). Peaks occurring frequently in wastewater influent, effluent and the receiving surface water, will be selected and identified.

Characterizing CECs distribution between activated sludge and water phase in wastewater treatment process will be done to better understand their removal by sorption. The task will be performed by equilibrating sludge sample suspension in presence of suitable partitioning passive samplers, analogous to work performed on PS of aquatic sediments. For testing passive sampling of CECs in sludge, representative samples of settled activated sludge will be collected from municipal WWTPs that have low to moderate industrial WW input. If successfully applied, the latter method will yield several endpoints, including activated sludge/water partition coefficients and accessible/releasable CEC fraction in sludge.

The dissertation will be partially performed in collaboration with an international team of PhD students and senior researchers from Masaryk University, Brno and the UFZ Helmholtz Centre for Environmental Research, Leipzig, within the research project “Accumulation in textiles and release by laundry as an emission pathway for aromatic amines from indoor environments to waste- and surface water” funded by Czech Science Foundation (GAČR) and the German Research Foundation (DFG).

Notes

CZ:

Sloučeniny vzbuzující obavy (CEC), jako jsou aromatické aminy, léčiva, přípravky osobní péče nebo v současnosti používané pesticidy, jsou považovány za nové třídy kontaminantů vody kvůli jejich prokázaným nebo potenciálním nepříznivým účinkům na vodní ekosystémy a lidské zdraví.

Cílem disertační práce je objasnit cestu vybraných CEC z různých emisních zdrojů v městských odpadních vodách až po jejich vypouštění do recipientu. Toho bude dosaženo kombinací různých přístupů k odběru vzorků životního prostředí a chemické analýzy městských odpadních vod.

Splaškové odpadní vody budou odebírány z kanalizačního systému před smícháním s ostatními přítoky odpadních vod. Kromě toho budou odebírány vzorky z přítoku do čistírny odpadních vod (ČOV), odtoku a po proudu recipient v souladu s hydraulickou dobou zdržení v ČOV, aby byla odebrána stejný „paket“ odpadních vod po cestě čištění. Vzorky budou odebírány pomocí pasivních vzorkovačů nebo jiných vhodných technik. Vzorky budou analyzovány hmotnostně spektrometrickými metodami s vysokým rozlišením a údaje budou podrobeny statistické analýze, aby bylo možné pochopit typické složení směsí CECs související se zdrojem, tj. píky představující určitý zdroj emisí CEC, jako jsou např. píky CES, které se vyskytují pouze v extraktech souvisejících s určitým typem zdroje (pomocí shlukové analýzy). Budou vybrány a identifikovány píky, které se často vyskytují v přitékající odpadní vodě na ČOV, odtékající odpadní vodě a v povrchové vodě, do níž se čištěná odpadní voda přivádí.

Bude provedena i charakterizace distribuce CECs mezi aktivovaným kalem a vodní fází v procesu čištění odpadních vod, aby bylo možné lépe pochopit jejich odstraňování sorpcí. Úkol bude proveden ekvilibrací suspenze vzorku kalu za přítomnosti vhodných rozdělovacích pasivních vzorkovačů, analogicky k práci prováděné při pasivním vzorkování vodních sedimentů. Pro testování pasivního vzorkování CEC v kalu budou odebírány reprezentativní vzorky usazeného aktivovaného kalu z komunálních ČOV, které mají nízký až střední vstup průmyslových OV. Pokud bude tato metoda úspěšně použita, získá se několik ukazatelů, charakterizujících distribuční koeficienty CECs v systému aktivovaný kal/voda a přístupné/uvolnitelné frakce CECs v kalu.

Disertační práce bude částečně řešena ve spolupráci s mezinárodním týmem doktorandů a vědeckých pracovníků z Masarykovy univerzity v Brně a Helmholtzova centra pro výzkum životního prostředí UFZ v Lipsku v rámci výzkumného projektu "Akumulace v textiliích a uvolňování praním jako emisní cesta pro aromatické aminy z vnitřního prostředí do odpadních a povrchových vod" financovaného GAČR a Německou výzkumnou nadací (DFG).

Supervisor

doc. Ing. Branislav Vrana, PhD.

Miniaturization and automation are key trends in modern experimental methods in the natural sciences and biomedicine. Microfluidics makes it possible to perform thousands of experiments per second thanks to the precise handling of nano- to pico-liter volumes of solutions in the microenvironment of channels measuring tens of micrometers. The project will focus on the development and optimization of microfluidic systems for high-performance characterization and study of proteins obtained from genomic databases and constructed by protein engineering methods. The obtained data will be evaluated by artificial intelligence methods. The newly developed methods will be applied in the study of the mechanism of Alzheimer's disease and the development of new drugs for stroke. The project will be solved in cooperation with the research group Prof. Andrew deMello at ETH Zurich, Switzerland (https://www.demellogroup.ethz.ch/) and the International Center for Clinical Research, University Hospital at St. Anny in Brno

Supervisor

prof. RNDr. Zbyněk Prokop, Ph.D.

CONTEXT: The intra-tumoral heterogeneity (ITH) represents a major challenge for effective cancer treatment and prognosis, as it undepins the differential responses to therapy and tumor progression. Understanding ITH on multiple scales (molecular, cellular, and tissue) and through various modalities (genomic, transcriptomic, proteomic, and imaging) is critical for advancing personalized cancer therapies.

OBJECTIVES: The main goal of the thesis is to advance the knowledge of ITH and to identify salient biological features characterizing the ITH of the colorectal cancers. To this end, it will integrate transcriptomics with morphological descriptors and immunohistochemistry to study and describe the tumor microenvironment and its local and less local interactions.

ADDITIONAL INFORMATION: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Assoc. Prof. Vlad Popovici (vlad.popovici@recetox.muni.cz) for informal discussion.

Supervisor

doc. Ing. Vlad Popovici, PhD

Project summary: Enzymes catalyse most of the chemical reactions that occur in biological systems and can be given non-natural catalytic functions by protein engineering. However, despite their vast importance, we do not know how enzymes acquire the structural diversity and conformational flexibility that enables them to evolve towards new molecular functions. Our proof-of-concept data on three structurally similar but functionally distinct enzyme classes of haloalkane dehalogenases (EC 3.8.1.5), beta-lactone decarboxylases (EC 4.1.1.114), and light-emitting monooxygenases (EC 1.13.12.5) suggest that as-yet-underexplored molecular elements – access tunnels and flexible loops – play a pivotal role in their functional diversification.

The proposed PhD project will investigate the molecular structures of these model enzymes using an innovative multi-method biology approach to identify the key structural and dynamic elements that govern enzymes’ evolvability. This project will combine X-ray crystallography, single-particle cryo-electron microscopy, and advanced mass spectrometry techniques to capture unprecedented molecular details of the conformational sampling that is required for productive enzymatic biocatalysis. Complementary protein simulations, mutational and biochemical experiments will delineate the evolutionary trajectories that lead to the emergence of novel enzymatic functions. The resulting knowledge will extend our understanding of molecular evolution beyond the current state-of-the-art, particularly by revealing how the conformational diversity of proteins is associated with specific biocatalytic functions. The gained knowledge from this PhD project will pave the way for the development of new theoretical concepts and cutting-edge software tools for the rational engineering of tailor-made biocatalysts exploitable in biotechnology and biomedicine.

PLEASE NOTE: Before starting formal application/admission process, all applicants are requested to contact supervisor (martin.marek@recetox.muni.cz).

Supervisor

Ing. RNDr. Martin Marek, Ph.D., MBA

The position’s field of research
The study of the host microbiome and immunity holds immense significance in the field of environmental toxicology. The intestinal microbiome-immunity system plays an important role in mediating the effects of environmental chemicals on an organism's health. Understanding this intricate host microbiome-immunity relationship is crucial as it can provide key insights into the mechanisms by which these chemicals negatively impact host organisms. The microbiome not only influences the absorption, distribution, and metabolism of toxic compounds but also serves as a critical modulator of the host's immune, endocrine, and neural system. With respect to the topic of the thesis, the deregulation of this microbiome-immunity system will be studied by combination of latest omics technologies including metagenomics and transcriptomics.
In this groundbreaking PhD position, the student will embark on an exciting adventure to study the impact of chemicals on the microbiome and immunity of zebrafish, a model organism that has revolutionized our understanding of vertebrate biology and environmental toxicology. The proposed research will focus on elucidating the impact of chemical exposure on zebrafish microbial communities, and how exposure to emerging chemicals affects this delicate balance between microbiome and immunity. The project will specifically focus on determination of the impact of the plastic additives and broad spectrum of microplastics. Such investigation is a part of larger international scientific projects, specifically PLASTsensing (https://planterastics.fkkt.uni-lj.si/plastsensing/) and EU PARC project (Partnership for the Assessment of Risks from Chemicals; https://www.eu-parc.eu/).

As a PhD researcher, you will embark on an exciting journey to:

• Employ cutting-edge molecular techniques, metagenomics, transcriptomics, and bioinformatics to unravel complex effect of studied organisms.
• Investigate the effects of chemical and microplastic exposure on zebrafish microbiome diversity and stability.
• Analyse the functional implications of microbiome alterations in response to chemicals and microplastics.
• Contribute to our understanding of how these findings impact the broader ecosystem and human health.

Supervisor

Mgr. Ondřej Adamovský, Ph.D.