Bioanalytical chemistry

Biomacromolecules help to detect and determine other biologically important molecules.

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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 goal of study is the preparation of highly-qualified specialists for research work in the field of Bioanalytical Chemistry in academic and company environments including the accredited laboratories. The student will get necessary theoretical background and skills to realize his/her own research project in a research group under the guidance of a supervisor and be able to evaluate the obtained results. Modern instrumentation and experienced personnel at the Department of Biochemistry and at cooperating institutions create unique opportunities for student to be involved in numerous research activities concerning development of instrumental bioanalytical methods (separation methods with various types of detectors; biosensors combining different biological components with divergent detection principles) and immunochemistry and molecular biology based methods. Simultaneously, the student will be performing literature search using all resources of Masaryk University libraries. The research covers a wide spectrum of biological levels from whole organisms to tissues, cells and individual proteins. The palette of possibilities is broadened through long-term cooperation with several research institutions at home and abroad. Biochemistry is marked by its open and interdisciplinary character, the classical biochemical approaches being frequently combined with methodology from other disciplines such as microbiology, molecular biology, informatics, and biophysics. This increases graduates’ adaptability and their ability to apply acquired skills in working life. He/she will be ready to prepare the scientific presentations and publications using modern software tools.

Practical training

Bioanalytical chemistry is dynamically developing field covering from biochemical, molecular biological and analytical approaches up the advanced experimental data evaluation. As many of the recent instrumentations and techniques are not available at the Department of Biochemistry, the students should during the doctoral studies spent some time at cooperating laboratories in Czech Republic or abroad. It should be taken as a form of practical training.

Career opportunities

Graduates of this doctoral degree program will be prepared for the work in the biochemical, pharmaceutical, medicinal and veterinary laboratories with the orientation both on the basic and applied research. They can work in the specialised accredited laboratories, that increase their possibilities of the perspective employment in Czech Republic and abroad.

They may continue their academic career at universities and research institutions both in the Czech Republic and abroad. They will be qualified for team member and leadership positions in scientific research and development at private firms and biochemical laboratories at a broad range of institutions specializing in human or veterinary medicine, pharmaceuticals, agriculture, and biotechnology. The professional specialization of the graduates is also compatible with further work in the field of environmental protection and with environmental movements and initiatives.

Admission requirements

Data from the previous admission procedure (1 Jan – 30 Apr 2020)

The aim of the admission procedure for this program is to search and select the best motivated candidates. The entrance examination has the form of an interview (or an online interview with foreign applicants), during which a committee of three academic staff evaluates professional experience, the ability to communicate in English and the motivation and readiness of the candidates.

Criteria for evaluation

The committee verifies and evaluates the level of professional knowledge and prerequisites of the candidate for independent scientific work in the field of doctoral research (0-200 points) and English language skills (0-100 points). To be accepted, the candidate must obtain at least 120 points in the expert part and at least 60 points in the language part of the examination. Before submitting the application, the candidate must consult with the potential supervisor the focus of his/her doctoral thesis, its topic is then specified during the first semester of study.

Application guide

Deadlines

1 Aug – 30 Nov 2020

Submit your application during this period

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Supervisors and dissertation topics

Supervisors

Dissertation topics

Single-subject studies

František Foret - Micro- and mezzo-fluidic instrumentation for enrichment of biological samples

Supervisor: Ing. František Foret, CSc.

OBJECTIVES: Development of instrumentation and methods for comprehensive and/or selective enrichment and analysis of nucleic acids, proteins and metabolites. The work will include electrophoretic and mass spectrometric instrumentation and will be focused on instrumental as well as methodological development of new techniques based on preliminary results obtained with an industrial partner.

FOCUS: Proof of principles of epitachophoresis for biology related samples; design and construction/modification of instrumentation for large volume sample processing. The topic is based on entirely new procedures currently in the state of patent application in the USA.

METHODS: epitachophoresis, MS, capillary electrophoresis and HPLC in combination with different detection techniques

LITERATURE: see WOS.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Ing. František Foret, CSc., e-mail: foret@iach.cz at CEITEC or Instute of nalytical Chemistry Academy of Science Czech Republic for informal discussion.

Host microbiome in relation to Barretts esophagus and esophageal adenocarcinoma development

Supervisor: doc. RNDr. Petra Bořilová Linhartová, Ph.D., MBA

OBJECTIVES: Along with individuals genetic predisposition, host microbiome is an important factor in etiopathogenesis of gastroesophageal reflux disease (GERD), increasing significantly risk of developing esophagitis (RE), Barretts esophagus (BE), and esophageal adenocarcinoma (EAC). The project aim is to determine markers at the level of microbiome, host genes and their interactions for earlier diagnosis/prediction of BE and EAC The project includes analyses of (1) metagenome and metatranscriptome at several sites of gastrointestinal tract (GIT) in GERD patients, (2) host exome and transcriptome in esophageal tissue in patients with BE/EAC, and (3) genetic profile of GERD patients. Mutations in patients exome/genome and gene expression levels in esophagus tissue will be correlated with microbiome.

FOCUS: The main objective of the study is to verify the applicability of molecular biologal approaches in the diagnosis and prediction of GERD complications, such as BE and EAC. Following our pilot data, an analysis of the upper GIT microbiome will be performed under physiological and pathological conditions, which may contribute to earlier diagnosis and optimization of the algorithm for secondary prevention measures in the development and treatment of BE and EAC in patients with GERD. The partial aims of the project: (1a) determination of microbiome in the oral cavity, esophagus, stomach and duodenum by metagenome sequencing method - and correlation with the results of Helicobacter pylori determined using qPCR 16S rRNA and/or culturing of this bacterium from biopsy tissue in patients with RE, with BE and with EAC. In the selected patients with BE and EAC in esophageal tissue with pathological findings vs without pathological findings we will perform: (1b) determination of bacterial transcriptome using sequencing techniques, (2a) analysis of selected parts of exome, and (2b) analysis of expression of selected genes. Further, we plan: (3a) to determine genetic predisposition from blood of the patients with RE, BE and EAC by determining the variability in specific genes involved in the function of the immune system and carcinogenesis.

MORE INFORMATION: https://webcentrum.muni.cz/med-upf/veda-a-vyzkum/tym-dr-petry-borilove-linhartove

PLEASE NOTE: For further information about the scientific content please contact the principle supervisor doc. RNDr. Petra Bořilová Linhartová, Ph.D. (peta.linhartova@gmail.com).

Identification of changes in glutamatergic pathways specific for sporadic form of Alzheimer's disease in human astrocytes

Supervisor: doc. Mgr. Jan Lochman, Ph.D.

OBJECTIVE: Neurodegenerative foldopathies represent a group of human protein-misfolding disorders that are characterized by a pathological alteration in conformation of a native protein which makes it resistant to degradation and leads to pathological gain and loss of function. These are followed by aggregation of the misfolded proteins into insoluble deposits. One of the most prominent protein-misfolding disorders is AD. The number of patients suffering dementia in the Czech Republic is estimated at 160 thousand. Up to two-thirds of cases are due to Alzheimer's disease, others include, for example, vascular dementia, Parkinson's disease or other degenerative brain disorders.

FOCUS: In neurodegenerative disorders (including Alzheimer's disease, AD) astrocytes/astroglia undergo complex changes that range from atrophy with loss of function to accumulation of reactive cells around disease-specific lesions (senile plaques in the case of AD). The cellular pathology of astrocytes in the context of human AD remains enigmatic; mainly because of severe limitations of animal models, which, although reproducing some pathological features of the disease, do not mimic its progression in full. The human induced pluripotent stem cells (hiPSCs) technology creates a novel and potentially revolutionizing platform for studying fundamental mechanisms of the disease and for screening to identify new therapeutic compounds.

EXAMPLE of a potential doctoral project - the student will focus on: Suitable procedures for studying early pathology of Alzheimer's disease (AD) are currently being sought. The main aim of the project is to create a model of cell cultures suitable for monitoring changes in the biology of nerve cells (neurons and astrocytes) in patients with AD. Using the induced pluripotent cell method (iPSC), the role of nerve cells in the formation of sporadic form of AD will be studied.

    The specific aims are following:
  • Analysis of DEGs (differently expressed genes) between patients and controls and measured physiological parameters in and between groups.
  • Analysis of DEGs (differently expressed genes) between patients and controls and measured physiological parameters in and between groups.
  • Verification of selected differences in genes expression by qPCR analysis.
  • Verification of very promising candidate genes expression by Western Blot.
  • Analysis of selected neurotransmitters by LC-MS/MS.

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Assoc. Prof. Jan Lochman for an informal discussion.

Jan Preisler - Applications of nanoparticles in mass spectrometry imaging

Supervisor: prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: Use metal nanoparticles as labels for sensitive mass spectrometry imaging. The method allows detection of a single molecule on a tissue section.

EXAMPLES of doctoral projects:

- Development of sample preparation protocol for specific detection of selected markers on sections of 3D cell aggregates or other tissues.

- Optimization of specific labelling with nanoparticles. The specificity will be based on antibody-antigen and avidin-biotin interactions, aptamer bindings etc.

- Development of nanoparticle detection schemes using inductively coupled plasma (ICP) and matrix-assisted laser desorption/ionization (MALDI) techniques.

- Study of nanoparticle transport efficiency in ICP MS. Confocal fluorescence or electron microscopy will be used as a reference method.

MORE INFORMATION: bart.chemi.muni.cz
Jan Preisler - Mass spectrometry imaging

Supervisor: prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: The dissertation projects focus on matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) for visualization of spatial distribution of biologically important compounds without chemical labelling.

EXAMPLES of doctoral projects:

- Development of sample preparation protocols for MALDI MSI. Samples may include 3D cell aggregates or other biological tissues.

- MALDI MSI of perifosine and other antitumor agents in 3D cell aggregates.

- Optimization of reactions on tissue sections. The aim will be, e.g., determination of double bond position in fatty acid chains in lipids.

MORE INFORMATION: bart.chemi.muni.cz
Pavel Kubáň - Developments and applications of novel microextraction techniques in analyses of complex samples

Supervisor: RNDr. Pavel Kubáň, DSc.

Experimentální část práce bude zahrnovat vývoj nových mikroextrakčních technik, které jsou založeny na selektivních přechodech analytů přes semi-permeabilní fázová rozhraní [1,2]. Při přechodu analytů bude využito difuze [1] nebo bude přechod urychlen účinkem elektrického pole [2]. Výsledné mikroextrakční techniky budou spojeny off-line nebo in-line s vhodnými analytickými metodami (primárně s kapilární elektroforézou) a adekvátnost takového spojení bude demonstrována analýzami biologicky, klinicky a toxikologicky významných analytů v reálných komplexních vzorcích jako je moč, krevní sérum/plasma a plná krev. [1] Kubáň, P., Boček, P., J. Chromatogr. A 1234 (2012) 2-8. [2] Kubáň, P., Šlampová, A., Boček, P., Electrophoresis 31 (2010) 768-785.

Petr Skládal - Nanoparticles for optical biosensors

Supervisor: doc. RNDr. Petr Skládal, CSc.

OBJECTIVES: The advanced nanomaterials as quantum dots (QD), photon up-converting nanoparticles (UCNP) and coloid metal nanoparticles (Au, Ag, Cu NP) will be combined with sensing systems as waveguides, optical and Raman microscopic set-ups, surface plasmon resonance transducers and other options in order to develop biosensing devices with enhanced sensitivity. Both static evaluation - analog response and scanning / tracking / discriminating approaches - digital response for single-molecules (object, cell, nanoparticle) detection will be evaluated.

FOCUS: The target analytes will include metabolites and clinical markers in body fluids (serum, saliva), food and drinks (allergens, contaminants, toxins) and infectious microbes (honey bee pathogens, Salmonella, Enterobacteria).

METHODS: Bioconjugation and immobilization of biomolecules, characterization of bioconjugates and biointerfaces, ink-jet based microarrays, scanning probe microscopies, design of biosensing devices, advanced optical techniques, scanning probe microscopy, signal acquisition and processing, chemometrics, software development.

LITERATURE: https://www.muni.cz/en/people/2202-petr-skladal/publications

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Petr Skladal (skladal@chemi.muni.cz) for informal discussion.
Zdeněk Glatz - Application of modern ambient ionization techniques mass spektrometry – DART a DESI v bioanalytical chemistry

Supervisor: prof. RNDr. Zdeněk Glatz, CSc.

OBJECTIVES: Ambient mass spectrometry (MS) offers the versatile group of techniques providing analysis of solid sample surfaces and liquids in an open atmospheric pressure environment. It provides fast, direct analysis of objects without any sample pretreatment with the use of the mass spectrometer. Direct Analysis in Real Time (DART) and Desorption electrospray ionization (DESI) will be used in this project for the important clinical and pharmacological studies. As a comparative methods Direct Injection (DI) and MS combination with the separation methods HPLC a CE will be used.

FOCUS: The target analytes will include drugs and their metabolites and clinical markers in body fluids (blood, serum, saliva).

METHODS: DART-MS and DESI-MS, capillary electrophoresis and HPLC in combination with different detection techniques – MS, UV-VIS, LIF, C4CD. A new sampling technique based on the dry blood spot will be used.

LITERATURE: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/publications

GRANT PROJECTS: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/projects

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Zdenek Glatz(glatz@chemi.muni.cz) for informal discussion.

Notes

Only one of the proposed theme will be finally occupied.

Zdeněk Glatz - Droplet mikrofluidics and its application in bioanalytical chemistry

Supervisor: prof. RNDr. Zdeněk Glatz, CSc.

OBJECTIVES: Droplet microfluidics offers significant advantages for performing high-throughput screens and sensitive assays. Droplets allow sample volumes to be significantly reduced, leading to concomitant reductions in cost and increasing of assay sensitivity. It combines these powerful features to enable currently inaccessible high-throughput screening applications, including single-cell and single-molecule assays.

FOCUS: The subjects of the study will be medicinally and pharmacologically important enzymes and the screening of their enzymes.

METHODS: droplet microfluidic system with the LIF detection, MS, UV-VIS, LIF, C4CD. A new sampling technique based on the dry blood spot will be used. Capillary electrophoresis and HPLC in combination with different detection techniques – MS, UV-VIS, LIF, C4CD will be used as supporting methods.

LITERATURE: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/publications

GRANT PROJECTS: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/projects

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Zdenek Glatz (glatz@chemi.muni.cz) for informal discussion.

Notes

Only one of the proposed theme will be finally occupied.

Study information

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

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