Environmental Health Sciences

For healthy future.

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Přijímací řízení do doktorských programů - akad.rok 2020/2021 (zahájení: jaro 2021)
Submission deadline until midnight 30 Nov 2020

What will you learn?

The programme integrates PhD topics of environmental chemistry, toxicology and risk assessment with related problems of analysis and modelling of big data produced in current research of environmental factors affecting health. The objective is to support independent development of young researchers that contribute to understanding of fundamental processes of chemical effects on health and ecosystems, considering the context of other external „exposome“ factors . The programme aims to prepare interdisciplinary independent personalities that are able – in addition to excellent knowledge in specific research topic - to understand practical use of their own research outputs. The programme will prepare graduates with outstanding profiles for both national and international labour market. The graduates have broad experiences with active communication in English (that is practiced during all study), carry other transferable skills and competencies learned through practical addressing of specific problems as well as own preparation and running of small projects.

PROGRAMME STRUCTURE: Programme is being prepared in both Czech and English versions. Czech programme is being administered in Czech language but even within this version, one of the objectives is strengthening of international competitiveness, which is supported by education and lectures in English. Studies are organized in two Specializations, where the differences are defined in requirements for theoretical State Doctoral Exam. Studies are available in presence form (which si the preferred variant) or combined form (offered to students that continue towards the defence of PhD after standard 4 years of studies, or – exceptionally – to external students). The combined form differs mainly in requirements on periodic weekly duties (such as seminars) and duties related to pedagogical competencies (contributions to education).

Practical training

Within dissertation projects students practically work on their own research projects and use various approaches depending on the focus of their works (laboratory experiments, field studies, analyses of samples and data from cohort environmental epidemiology studies, programming and development of techniques of data modelling). A part of the study duties is the practical stay abroad or other form of international practical training.

Further information

http://www.recetox.muni.cz/

Career opportunities

Graduates will be able to successfully work within national and international set up at institutions and universities running research programmes on chemical contamination and other environmental factors affecting ecosystems and human health, including related fields of big data analyses, mathematical biology, bioinformatics and biomedicine. In addition to research, graduates may aim to institutions involved in safety assessment and control of various environmental matrices, food safety and risk assessment. Graduates of the programme may also actively work in the organizations controlling chemical risks, in laboratories or research departments of innovative biotechnological enterprises, in companies focusing on environmental technologies including bioremediations or in the regional or governmental authorities.

Admission requirements

Qualities of the candidates are checked during interview (can be online e.g. via skype). Committee assesses expertise and motivation for independent scientific work (0-200 points) and ability to communicate in English (0-100 points). Successful candidate must have minimum 120 points for the expert part and minimum 60 points for the English language check. Expert part requirements: Discussion on broader topics of the Environmental Health Sciences considering future specialization (Environmental chemistry and toxicology; Computational biology, modeling) Language part equirements: Communication skills – interview in English.

Application guide

Deadlines

1 Aug – 30 Nov 2020

Submit your application during this period

Submit an application

Study options

Single-subject studies with specialization

In the single-subject studies, the student deepens knowledge in the concrete focus of the degree programme and chooses one specialization. The specialization is stated in the university diploma.

Supervisors and dissertation topics

Supervisors

Dissertation topics

Specialization: Computational biology, bioinformatics and modelling

Machine Learning for Computer-Guided Protein Design

Supervisor: prof. Mgr. Jiří Damborský, Dr.

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.

Mass spectrometry of human exposure and metabolism

Supervisor: prof. RNDr. Jana Klánová, Ph.D.

Over the past decade, technological developments of high-resolution mass spectrometry (HRMS) has enabled full-scan “non-target” screening of chemical mixtures in complex matrices to achieve simultaneous measurement of hundreds of exogenous contaminants per sample (i.e. chemical exposomics), alongside endogenous metabolites (i.e. metabolomics).
Due to the relative maturity of metabolomics, current pipelines for the analysis of HRMS chemical profiling data are mostly designed for endogenous measures and need adaptation to be better suited for exogenous chemical exposures. In particular, these adaptations are required because typical metabolomics data analysis workflows rely upon mapping compounds to biological pathways (based on genome reconstructions /reference biosynthetic pathway maps) and thus are not applicable to exogenous compounds.
Furthermore, measures of chemical exposures are inherently more variable than for endogenous compounds, both qualitatively (detection frequency) and quantitatively (abundance), leading to wider distributions and greater sparsity of measurements. As such, quality assurance/ quality control (QA/QC) procedures need to be further refined to ensure reproducibility during large-scale population studies, including reproducible data processing.
Galaxy is a leading open-source bioinformatics workflow platform that provides a transparent, accessible and reproducible framework for implementation of complex analytical pipelines in a modular format. At present, there are two Galaxy pipelines for MS metabolomics data: Workflow4Metabolomics (W4M) & Galaxy-M yet, neither are specialised for chemical exposure data. Notably, dedicated tools for processing GC-HRMS measures of exposures are lacking.

Outside of the Galaxy framework, specific tools for analysis of environmental exposures have recently been developed. However, typically these specialised tools are not user friendly (mostly within R) and/or do not align with the available metabolomics pipelines (using different ontologies, reporting standards, databases and repositories etc.).

Therefore, the PhD project will encompass the development of resources for GC-HRMS data processing applicable for both metabolomics & chemical exposure measures with subsequent incorporation into the user-friendly Galaxy environment.

Modeling of prenatal and early childhood exposure to organic pollutants

Supervisor: Mgr. Klára Komprdová, Ph.D.

Elevated levels of pollutants can negatively affect children's development in their first years of life. Research goal is modeling of children’s prenatal and postnatal exposure to organic compounds, that can significantly affect early (neuro)development. Another goal is to identify the effect of socio-economic, diet and physiological factors on increased concentrations of pollutants in mothers and children.

The project focuses on statistical analysis of human biomonitoring data (e.g. relationship between concentrations of compounds in cord blood, maternal blood, breast milk or urine and life-style factors in mother-child cohort), and mainly on development of pharmacokinetic models to estimate the distribution of pollutants and their time trends in target tissues. Estimated concentrations of pollutants in tissues will be compared with critical values for which an effects on the mental and motor development of children exposed to these substances has been found. Modeling includes also simulation of chemical’s distribution under different conditions, calculations of intake in time during exposure and identification the main exposure sources. The student will be also involved in the development of models towards the prediction of the potency and specific mechanisms of action of studied pollutants related to their potential adverse effects in population, using namely quantitative structure relationship methods. These approaches will be used for prioritization of risk drivers and also in predictions of the specific toxic potentials of relevant exposure mixtures.


PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Klara Komprdova (klara.komprdova@recetox.muni.cz) for informal discussion.

Specialization: Environmental chemistry and toxicology

Adverse Outcome Pathways and mechanistic toxicology of emerging chemicals and their mixtures

Supervisor: prof. RNDr. Luděk Bláha, 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.
An impact of ambient air pollution on human diseases

Supervisor: prof. RNDr. Jana Klánová, Ph.D.

Ambient air pollution is considered to be one of the most important factors significantly increasing morbidity and mortality of various chronic diseases. This dissesrtation project will assess an impact of polluted air on various health conditions with a special focus on chronic conditions. The project will utilize longitudinal data from the regional population studies such as the Central European Longitudinal Study of Parents and Children (CELSPAC) or Health, Alcohol and Psychosocial factors in Eastern Europe (HAPIEE).

Associations between environmental and social stressors and population health in the cohort studies (CELSPAC, HAPIEE)

Supervisor: Mgr. Hynek Pikhart, Ph.D., M.Sc.

The advertised positions will focus on environmental epidemiology. The successful candidates will investigate associations between environmental and social stressors and population health in the extensive prospective cohort studies (CELSPAC, HAPIEE) in the Czech Republic using multivariable regression techniques.

The selected Ph.D. students will join a newly established ERA Chair Team (https://www.recetox.muni.cz/erachair) supported by the competitive Horizon 2020 ERA Chair project R-EXPOSOME.

Comprehensive investigation of indoor chemical exposures

Supervisor: Lisa Emily Melymuk, Ph.D.

There is a complex mix of chemicals in all indoor environments, and these are important sources of chemical exposure to humans. This project will screen indoor environmental matrices (air, dust, consumer products) to assess the mixture of chemicals in residential and other indoor environments, and synthesize data from different geographic regions and types of environments to determine key sources of variability, the impact of differing chemical regulations, and prioritize which compounds we should be focusing on for further risk analysis and toxicity evaluation. The project comprises review of current data combined with targeted analysis and suspect screening of indoor samples to profile the chemical mix indoors, followed by prioritization of the identified chemicals according to regulations, levels and hazard.

Endocrine disrupting potential of relevant exposure mixtures and prioritized pollutants

Supervisor: doc. Mgr. Klára Hilscherová, Ph.D.

OBJECTIVES: The overall research goal is to develop efficient approaches for the characterization of specific toxic potentials of complex exposure mixtures that organisms including human are exposed to in the environment. This refers to the realistic exposure scenarios with possible joint action of a wide spectra of pollutants. The research aims namely on the ability of pollutants to interfere with hormonal regulation (endocrine disruption) and the role of this disruption in adverse effects, especially on the early (neuro)development and reproduction. The outcomes will help to prioritize the toxicity risk drivers, characterize the joint action of co-occurring chemicals and relationship of the mixture exposure with adverse effects in exposed organisms including human. This will provide scientific basis for effective risk and regulatory assessment and management of relevant exposure mixtures and chemical risk drivers and thus contribute to environmental and human health protection.

FOCUS: The doctoral research projects focus on development and implementation of diagnostic and predictive effect-based methods (in vitro, in silico) for the characterization of potential impact of internal and external exposure mixtures on environmental and human health and associated risks. This includes description of relevant exposure mixtures effects on key processes in hormonal regulation affecting early (neuro)development and reproduction in organisms. Adverse outcome pathways concept will be employed to relate the in vitro/in silico assessed endocrine disrupting potential with diagnostic approaches on the level of effect biomarkers or omics methods linking the mechanisms of action with these disorders. The projects will focus namely on the development and optimization of a battery of high-throughput bioassays covering wide range of modes of action relevant for neurodevelopment or endocrine disruption, and characterization of the endocrine disrupting potential of complex environmental exposure and effect-driver identification by a combination of progressive bioanalytical, molecular biology and non-/target high-resolution mass spectrometry methods.

EXAMPLES of potential student doctoral projects:

(1) Endocrine disrupting pollutants able to interfere with early development

(2) Adverse outcome pathways-based approaches in human exposure and epidemiological studies

(3) Human cell-based bioanalytical approaches for the assessment of endocrine disruptive potential including 2D and 3D-in vitro systems

(4) Assessment of biomarkers of endocrine disruption in biological matrices using advanced analytical methods and their relation to exposure

MORE INFORMATION: www.recetox.muni.cz

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are recommended to contact Assoc.Prof. Klára Hilscherová (hilscherova@recetox.muni.cz) for informal discussion and more information on the PhD studies and research topics.

Influence of the built environment on human exposure to chemicals

Supervisor: Lisa Emily Melymuk, Ph.D.

We spend the majority of our time in indoor and urban spaces, and these areas are known to both positively and negatively impact human health. Chemical exposure is one element of the exposome that can be both positively and negatively impacted by the built environment. This project will use chemical screening and data analysis methods to characterize profiles of anthropogenic chemicals in the built environment (e.g., indoor dusts, indoor air, outdoor air), link this chemical data with lifestyle and built environment characteristics, and synthesize this knowledge to improve our understanding of the potential impact on human health.

Metabolomic and toxicokinetic approach to improve in vitro toxicity assessment and in vitro-in vivo extrapolation

Supervisor: RNDr. Iva Sovadinová, Ph.D.

The topic will focus on the use of metabolomic and toxicokinetic approach and tools to study in vitro effects of toxicants and to improve in vitro-in vivo extrapolations.

Strategies for small-volume chemical exposure analysis

Supervisor: prof. RNDr. Jana Klánová, Ph.D.

The PhD candidate will develop strategies for the analysis of internalised chemicals in biofluids via high-resolution mass spectrometry (HRMS) chemical profiling. Despite advances in HRMS technology, broad detection of low-abundant chemical exposures from small volume samples still poses significant challenges. Selective enrichment procedures will be investigated with a particular emphasis on feasibility & scalability for application to large-scale cohort studies.

Required expertise: biochemistry, analytical sample preparation, mass spectrometry

Candidate profile
Candidate shall possess a Master’s degree within biochemistry and excellent lab skills. An eagerness to learn broader systems biology and exposure science is beneficial. Good communication skills in English language are required.

Structural and biochemical studies of engineered enzymes

Supervisor: Ing. RNDr. Martin Marek, Ph.D.

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).

Study information

Provided by Faculty of Science
Type of studies Doctoral
Mode full-time Yes
combined Yes
Study options single-subject studies No
single-subject studies with specialization Yes
major/minor studies No
Standard length of studies 4 years
Language of instruction Czech
Collaborating institutions
  • The Czech Academy of Sciences
  • Ústav výzkumu globální změny AV ČR
Doctoral board and doctoral committees

Do you have any questions?
Send us an e-mail

prof. RNDr. Luděk Bláha, Ph.D.

Consultant

E‑mail: