PhD studium

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 well in advance of the PhD defense (ideally 1 year) and 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 student will prepare 1 page report about the state of her/his project and will submit the PDF version of the report to the chairman of the Programme Board at least one week before the exam. Two examples for inspiration are here: 1 and 2.
3. 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.
4. 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.

The student is ready to take the state doctoral examination after fulfilling all study obligations, i.e., completing theoretical preparation courses, fulfilling the obligation of language competence, obligations related to pedagogical development, i.e. in the middle of the standard period of study. The student takes the state doctoral examination during the 5th or at the latest the 6th semester of study. The State Doctoral Examination takes the form of an interview in which the candidate demonstrates a general orientation in the field and the ability to communicate and discuss with the examiners. State Doctoral Examination Circuits:

- Structure and molecular principles of microbial, plant and animal cells and their viruses
- Mechanisms of mutagenesis, recombination, transposition and DNA repair
- Molecular basis of carcinogenesis
- Principles of cell signalling
- Characteristics and applications of stem cells
- Principles of proliferation control, differentiation and cell death
- possibilities of genetic engineering and gene therapies
- genomics and proteomics
- molecular basis of inherited diseases
- general, molecular and developmental genetics
- medical genetics and cytogenetics
- genetics of quantitative traits
- plant genetics
- animal genetics

Recomended literature:
SNUSTAD, D. Peter, Michael J. SIMMONS, Jiřina RELICHOVÁ, Jiří DOŠKAŘ, Jiří FAJKUS, Petr HOŘÍN, Aleš KNOLL, Petr KUGLÍK, Jan ŠMARDA, Jana ŠMARDOVÁ, Renata VESELSKÁ a Boris VYSKOT. Genetika. 2. akt. vyd. Brno: Masarykova univerzita, 2017. 864 s. Učebnice. 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.

When preparing their dissertation, the student must choose one of the following two formats and explicitly indicate this choice in their application for the defense:

A) Full-text Dissertation

• Represents a comprehensive treatment of the dissertation topic.

• Must include the following chapters: Introduction, Literature Review, Aims of the Study, Materials and Methods, Results, Discussion, Conclusion, References.
  (Note: the Results and Discussion chapters must not be merged.)

• The student’s publications are not part of the dissertation text itself, but a list of these publications must be included (see Dean's Measure 2019/8).

• All experimental data presented must be included in the Results chapter.

• Publications related to the dissertation topic are submitted separately to the defense committee as additional documents and must be delivered to the R&D Office together with the dissertation.

• The expected minimum length of this type of dissertation is 80 pages of text (excluding the list of references), using standard formatting: Times New Roman 12 pt or equivalent, 1.5 line spacing.

B) Commented Collection of Publications

• Consists of a coherent set of at least three original research articles authored or co-authored by the student, covering the topic of the dissertation. Review articles may be included but do not count towards the minimum of three original articles.

• Must include the following chapters: Introduction, Literature Review, Aims of the Study, Results and Discussion (merged into a single chapter), Conclusion, References.
  (This merged chapter should present the results in the context of previously published findings, and references to specific articles should also be included when discussing the student's own results.)

• The Materials and Methods chapter is omitted, as relevant methodological information is expected to be part of the included publications.

• Only published articles or manuscripts already submitted for peer review may be included. Unsubmitted manuscripts cannot be part of the dissertation. For submitted manuscripts, proof of submission must be provided to the R&D Office.

• For each publication, the student must state their percentage of authorship, and must also submit a separate authorship contribution form, confirmed by the supervisor and corresponding author, listing the percentage contributions of all co-authors. This form must be submitted along with the dissertation to the R&D Office.

• A complete list of the student’s publications and conference presentations must be included.

• The expected length of this type of dissertation is 30–40 pages of text (excluding references and attached articles), using standard formatting: Times New Roman 12 pt or equivalent, 1.5 line spacing.

Minimum Requirements for Submission

To submit the PhD thesis for defense, at least part of the results must be published or accepted for publication in an international peer-reviewed journal with an impact factor above the median of the field, where the student is the first author.
An alternative option is to include at least two articles (with at least one first-author paper) published in journals with an impact factor of 1.0 or higher, regardless of the field median.

If the articles or manuscripts included in the dissertation were written in collaboration with co-authors, the doctoral candidate must clearly define their individual contributions in the dissertation.
Publication in an international peer-reviewed journal cannot be substituted by other forms of academic communication (e.g., conference contributions, abstracts, etc.).

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).