study requirements

The State Doctoral Examination is oral and includes a test of the candidate's theoretical knowledge in the topics Anatomy and Cytology of Plants, Plant Physiology, and Ecological and Stress Physiology of Plants. The questions cover topics of subjects taught at the Faculty of Science of MU in the Master's and Doctoral studies in the field of experimental plant biology, i.e. subjects taught mainly at the home department of OFAR ÚEB of the Faculty of Science of MU.

The student may take the SDZ at the earliest in the 5th semester of study and after fulfilling the above-described obligations. The table below summarizes the mandatory obligations, their required minimum and timing. Exceptions in justified cases are approved by the Programme Board.The SDZ takes place consists of these steps:

1. The first step is to announce the intention of the student to take the SDZ to the chairman of the Programme Board and to the study department.
2. The SDZ consists of the presentation of the PhD project – within a maximum of 20 minutes, the student will present his/her research project, its hypotheses and the data he/she has so far, their evaluation, conclusions, and suggestions for further steps. This presentation has a preliminary form of the future dissertation defense.
3. In the follow-up discussion with the SDZ committee, the student should prove the ability to apply his/her knowledge to solve specific problems and demonstrate good orientation in the fields involving the scientific problem investigated in the doctoral thesis. The discussion will be focused on the students’ research work.

SDZ committee will evaluate:

• overall knowledge of the topic including broader context and meaning
• ability to explain and present their work
• knowledge of hypothesis and methods of solution
• knowledge of experimental techniques, focusing on the ability to choose an optimal experimental approach
• ability to correctly interpret data, draw and discuss conclusions

The theoretical state doctoral examination takes place at the earliest in the 5th semester and after the required obligations set out in the individual study plan (ISP) have been fulfilled (e.g., knowledge-enhancing courses, seminars, teaching assistance, theses, soft skills). It takes place before a five-member committee of experts approved by the MU Faculty of Science and at least two of the committee members are external students.

To be eligible to undergo the SDE, students must have fulfilled all study requirements, including completion of theoretical coursework and compulsory seminars (semesters 1–4 of study), participation in the Control Day after the second year of study, and teaching obligations (see: /do/sci/web/vzd/studijni_plany/MBBG.pdf). Students register for the SDE through the Information System (IS). It is recommended that the intention to apply for the SDE be discussed in advance with the Chair of the Doctoral Board.
The State Doctoral Examination takes the form of an oral examination, during which candidates demonstrate a comprehensive overview of the field as well as the ability to communicate and discuss professionally with the examiners.

Examination topics include:
- structure and molecular principles of microbial, plant, and animal cells and viruses
- mechanisms of mutagenesis, recombination, transposition, and DNA repair
- molecular basis of carcinogenesis
- principles of cellular signaling
- characteristics and applications of stem cells
- regulation of cell proliferation, differentiation, and cell death
- genetic engineering and gene therapy
- genomics and proteomics
- molecular basis of hereditary diseases
- general, molecular, and developmental genetics
- medical genetics and cytogenetics
- genetics of quantitative traits
- plant genetics
- animal genetics

Recommended study literature includes, for example:
Alberts B. et al. Molecular Biology of the Cell. 7th edition. W. W. Norton & Company, 2022. ISBN 978 0393388482.
Snustad, D. P., Simmons, M. J., Relichová, J., Doškař, J., Fajkus, J., Hořín, P., Knoll, A., Kuglík, P., Šmarda, J., Šmardová, J., Veselská, R., & Vyskot, B. Genetics. 2nd revised edition. Brno: Masaryk University, 2017. 864 pp. ISBN 978 80 210 8613 5.

In every semester, enrol the course XD100: Ph.D. Thesis (obligatory in each semester, 25 ECTS for semesters 1-4, 30 ECTS for semesters 5-8, 20 ECTS for semesters 9+). The total credit value of XD100 during the study should be between one-half and two-thirds of the minimum credit value of the study, i.e. 120-160 credits for a four-year study.

The doctoral thesis has to be based on student´s own and original scientific results and a necessary prerequisite for its acceptance in the program of the Animal Physiology, Immunology and Developmental Biology is that its most significant results should be published or accepted for publication in international peer-reviewed professional journals (registered in the ISI Journal Citation Reports database).

Minimum criteria for publications:

• 1 paper as a first author in journal in the Q1 or Q2 according to Journal Citation Reports
• at least 1 more paper as co-author (obligatory minimum but for a good grade you need more)
• If the articles and manuscripts contained in the thesis are written with co-authors, then the student must clearly define his/her specific share in each of them (not only the percentage).

In cases of shared first-authoring, the Doctoral Committee will apply generally stricter standards for the quality of publications.

In very exceptional cases, for example, an exceptionally high-quality publication that is associated with a long review process, some of the conditions may be waived. In this case, the Doctoral Committee will assess the written request of the supervisor and may approve the acceptance of the thesis for defense.

The preferred form of the doctoral thesis is a set of published articles or manuscripts accepted or ready for publication. A doctoral thesis in this form usually contains three articles (minimum two) or manuscripts of articles supplemented with an introductory chapter of an extent of 20 pages minimum, which will

• logically link the individual articles and put them in the context of contemporary knowledge
• define the main aims that the author of the thesis has set for him or herself
• evaluate the importance of the results achieved for the respective field

In this introductory chapter, the PhD students have to demonstrate their professional overview and a wider orientation in the given field than only in the specialized topics of individual articles.

Formal requirements on the PhD thesis:

• Official formal requirements for the thesis (CZ)
• Official formal requirements for the thesis (EN)
• The only acceptable language is English.
• The introductory essay contains the sections Introduction, Overview, Objectives, Results and Discussion, Conclusion, Literature.
• Material and methods need not be included since sufficient information should be included in the annotated publications in the Annex.
• The Results and Discussions are, from the point of view of the significance of the work, the main chapters whose purpose is to present own achieved results in the context of already published knowledge; in the text, the doctoral student must prove his / her professional perspective and broader orientation in the field.
• The supposed extent of the dissertation is equivalent to 30-40 pages (without a list of literature and without attached articles) of standard format New Times Roman 12b., spacing 1,5.

The dissertation must contain original results that have been published or accepted for publication. The dissertation is prepared in English, and the student may submit it in one of two formats (a full-text dissertation or a commentary on an annotated set of publication). The chosen format must be explicitly indicated in the application for the dissertation defence in the Information System.

 Full-text dissertation

- presents a comprehensive study of the assigned dissertation topic

- must obligatorily include the following sections: Introduction, Aims, Materials and Methods, Results, Discussion, Conclusion, References (the Results and Discussion sections must not be combined)

- all experimental data presented must be included in the Results section

- the dissertation must include a list of the student’s publications, specifying the percentage contribution of the student’s authorship and a description of the student’s individual contributions to each publication (template according to Dean’s Measure 2019/8, available at https://is.muni.cz/auth/do/sci/normy/OP/OD19-08/OD_8_2019_EN_Guidelines_for_Doctoral_Theses_SCI_MU.pdf, supplemented with percentage contributions for each publication)

- the expected minimum length of this dissertation format is 80 pages of text (excluding references), using standard formatting: Times New Roman, 12‑point font (or equivalent), 1.5 line spacing

Annotated set of publications

- represents a coherent collection of at least three published original scientific articles to which the student has made an authorship contribution and whose content covers the assigned dissertation topic; the collection may also include review articles, however, such articles are not counted toward the minimum requirement of three original articles

- must obligatorily include the following sections: Introduction, Literature Review, Aims, Results and Discussion, Conclusion, References (the Results and Discussion sections must be combined into a single chapter, the purpose of which is to present the achieved results in the context of existing published knowledge; references to specific publications must also be provided)

- the Materials and Methods section is not included, as sufficient methodological details are expected to be provided in the commented publications

- only articles that have already been published or manuscripts that have been submitted for peer review may be included in the commented collection (manuscripts that have not yet been submitted cannot be included); in the case of submitted manuscripts, confirmation of submission for peer review must be provided to the Chair of the Doctoral Board

- the dissertation must include a list of the student’s publications, specifying the percentage authorship contribution and a description of the student’s individual contributions to each publication (template according to Dean’s Measure 2019/8, available at
https://is.muni.cz/auth/do/sci/normy/OP/OD19-08/OD_8_2019_EN_Guidelines_for_Doctoral_Theses_SCI_MU.pdf, supplemented with percentage contributions for individual publications)

- the expected length of this dissertation format is 30–40 pages of text (excluding references and appended articles), using standard formatting: Times New Roman, 12‑point font (or equivalent), 1.5 line spacing

The defence of the doctoral dissertation consists of a 20-30 minute oral presentation in which the candidate briefly describes the theoretical background and hypothesis(es) of the thesis, the methods used, the results obtained and their interpretation. The candidate then answers the questions raised in the referees' reports. The referees present will comment on the candidate's answers individually. This is followed by a theoretical debate in which the members of the examination committee, the CoR and the professional and lay public present at the defence raise questions (related to the topic of the thesis and the presentation) with the candidate, who answers these questions directly.

The evaluation of the candidate(s) is immediately thereafter carried out by secret ballot by the members of the committee with voting rights. Immediately after the votes have been counted, the candidate is informed of the results of the vote and the outcome of the SDZ.

The first formal step of the defense is to announce the intention to do so by the student to the chairman of the Programme Board and the study department.

The PhD thesis must be submitted to the study department at least 8 weeks prior to the planned defense. Students also elaborate self-report/summary of the final thesis, which they send in PDF version to the chairman of the doctoral committee at least one week before the defense (student can enrol and get credits for BD010: PhD Thesis). Two examples of the self-report/summary for inspiration are here: 1 and 2.

The work will be judged by 2 opponents, at least one being from a workplace outside MUNI. It is expected that at least one of the opponents will be from abroad. The presentation during the defense has a maximum duration of 25 minutes, followed by the statement of two opponents based on written reviews and their discussion with the student. In case of a dissertation that meets just the minimum requirements, the Doctoral Committee assesses the overall quality of the results and the dissertation thesis particularly carefully and critically and generally evaluates the result with a reduced grade. The PhD defense is conducted in English.

Informatively, we add the instructions that are given to the PhD thesis opponents: PhD Thesis Defense at OFIŽ

The defence of the dissertation (in the form of annotated publications or full-text) takes place again in front of a five-member committee plus at least two thesis opponents. It is possible to submit the thesis for defence if other study obligations are fulfilled in the second half of the study (seminar, foreign stay, lecture at an international conference, publication).

The first formal step of the defense is to announce the intention to do so by the student to the chairman of the Programme Board and the study department. For the dissertation defense, the Doctoral Board appoints a committee composed of experts in the relevant research area. The dissertation is assessed by two independent external reviewers. The defense begins with a brief introduction of the candidate by the Chair of the committee, followed by the candidate’s presentation, with a duration of 25 minutes. The presentation should include a concise introduction to the research topic and a summary of the most important results. This is followed by presentation of the evaluation reports, first by the supervisor and subsequently by the reviewers. IN the following discussion with the reviewers, the student responds to their comments and questions. Subsequently, the student also answers questions posed by other members of the committee and by the audience. At the end of the defence, the committee decides whether the defense has been successful.