PhD study

Content:

General information

General information on PhD study is available at the Faculty website.

The current Experimental Plant Biology board is listed in SIS.

 

Principles of PhD study

The key duty of doctoral students in the study program (SP) of Experimental Plant Biology (EPB), which is the successor of the SP Plant Anatomy and Physiology (PAP) since the academic year 2020/2021, is an active scientific activity in the subject of their dissertations and deepening professional knowledge of plant biology. The primary goal of doctoral studies is to master the methods of scientific work and thinking so that the graduate can independently identify and solve scientific problems, critically assess the results, and process them for publication in internationally recognized scientific journals.

The Board for PhD Studies in EPB (BS EPB) sets the rules, supervises the course of study, and evaluates the outcome. The current composition of the BS EPB can be found here – members of the Board for PhD Studies.

The doctoral study of the EPB program is accredited jointly for the Faculty of Science of Charles University and the Institute of Experimental Botany of the Academy of Sciences of the Czech Republic.

 

Application and entrance exam

If you are interested in studying experimental plant biology (EPB), choose an area of research that is carried out at the Department of Experimental Plant Biology, Faculty of Science, Charles University (CUNI) or one of the cooperating institutes (Institute of Experimental Botany Czech Academy of Sciences (CAS), Institute of Botany CAS, or Research Institute of Crop Production), contact a potential supervisor and agree on a specific research topic and the possibility of financial compensation for the proposed research carried out within the PGS (including institutional resources). Potential thesis topics can be found in SIS, but the final topic is usually „tailor-made“ after discussion and agreement between the supervisor and student. The application for doctoral studies in the spring term must be submitted by April 30. If the second admission date is announced, it is necessary to follow the dates published on the website of the Faculty of Science, Charles University.

Information for new potential supervisors:
Those interested in supervising in the field of experimental plant biology at the Faculty of Science, Charles University, who have not been a supervisor on the EPB Board (or previous OR Plant Anatomy and Physiology), contact the EPB Board Chairman (Prof. Jana Albrechtová, albrecht@natur.cuni.cz). New supervisors are approved by the BSEPB and the Scientific Board of the Biology Section - for approval it is necessary to submit a CV, including grants, publications, and teaching activities. The proposed research topic must fit into the broader field of experimental plant biology and the supervisor must guarantee financial coverage of the planned research (from the project or institutional funds). Ideally, the supervisor can contribute to the student’s scholarship or offer additional employment.

Entrance exam (recommendations of BS EPB):

  • Current conditions for the admissions process here.
  • The student must take an entrance examine unless they are excused (the test may be taken remotely after approval).
  • Principles for evaluating entrance exam performance:
    • The committee evaluates the quality and presentation of the dissertation project. The applicant may add their project abstract to the study application in the form of an optional attachment, or bring it with them to the interview. Both the scientific merit and presentation of the topic, as well as the applicant’s responses to the committee’s questions are evaluated. Abstracts should be prepared in cooperation with the intended supervisor.
    • The committee also evaluates the knowledge and orientation of the candidate in their field of study, especially regarding the topic of their dissertation, previous professional experiences (i.e. a Master’s degree), and personal motivation. The candidate must demonstrate knowledge of current scientific issues in their field (especially concerning their project), the ability to ask relevant questions, formulate hypotheses and evaluate them critically.
    • The committee may also take previous professional experience and academic outcomes into consideration.
  • The candidate, together with their intended supervisor if present, will also be asked about their source funding for the proposed scientific work.

 

Course of study and reporters' system

The applicant becomes a doctoral student on the day of enrolment at the faculty.

BS Experimental Plant Biology (EPB) introduced the reporters' system, which aims to facilitate the successful course of study. At the beginning of the study, the BSEPB will assign two of its members to the student as reporters. The reporters are introduced to the student at the beginning of their study and monitor the status of the dissertation from its admission to the study. At least once a year, in person or through distance communication, they consult with the student on the progress of their work, their cooperation on a team, and discuss the possibilities of successful completion of the work and its defence. The student includes feedback from the reporters in the text of their annual ISP.

The reporter is present in person or remotely (by teleconference) at student presentations during the study. They represent an external view of the dissertation topic and can thus help improve the students’ quality of work and study with suggestions and comments. The reporter does not have the right to interfere in the intentions the work, the training team, or the student, but can act as a consultant if there is a mutual agreement. During the annual evaluation, they monitor the student’s ISP and provide an evaluation.

1st year – at the start of studies:

If the student would like to communicate with the OR during their studies, they should contact their reporters or the current chairman of the OR.

Individual Study Plan (ISP):

Upon admission, the student prepares an individual study plan (see form in SIS) in cooperation with their supervisor, the head of the laboratory where the work will be completed, and the chairman of the board. The plan contains a brief description of the intended experimental work and a list of planned study obligations (maximum 5), which must be fulfilled before applying for the State Doctoral Examination (SDE). The selection of lectures and practical courses is determined by agreement between the supervisor and the doctoral student, considering previous studies. In the case of students who obtained Mgr. degree at the Department of Experimental Plant Biology (DEPB) of the Faculty of Science, Charles University or completed content-related studies elsewhere, no subjects need be included in the study obligations, students from other fields are expected to have a more extensive study plan to supplement/unify knowledge). A formal English exam is not required. However, doctoral students are expected to know English to the extent necessary for normal scientific communication, both in writing and orally. The student demonstrates knowledge of English, among other things, during the presentations of his results, which are compulsory from the 3rd year in the form of lectures in English. The ISP includes at least one poster and one oral presentation in English at the conference (including student conferences, i.e. organized by the Czech Society of Experimental Plant Biology, where students choose the form of presentation). The study plan is approved by the BS EPB. The study plan should be designed for the study to successfully complete their doctoral studies (i.e. defend their thesis) by the end of the 4th year.

Research Project - detailed ISP:

During the 1st year (within the deadlines set by the BS EPB) the student, with guidance from their supervisor, submits a detailed written plan of their experimental plan for the BS EPB. The document should be between 2-3 pages in length, including a brief introduction to the issue, goals and hypotheses, the experimental methods (procedure, methodology), citations of literature and a detailed experimental plan for the 1st year of work on the project. The list of citations is not included in the length. The student also consults their project plan with their reporters. It is recommended to structure the detailed ISP like a GAUK proposal so that is can later be adapted for grant applications. BS EPB welcomes the submission of a grant project by the end of the summer semester of the 1st year of study or supports the submission in the 2nd year of study, where the student is the main researcher (GAUK) or a member of the research team with a clear definition of the share (Czech Grant Agency, etc.).

The research project will be archived by the BS EPB and used as a basis for the evaluation of the student by members of the BS EPB, including reporters with whom the student regularly consults about the progress of their experimental work.

Presentation of the research project – detailed ISP:

After submitting the research project - a detailed ISP in the 1st year, the student presents (within the deadline set by the BS EPB the plan of his research project. The presentation relates to the BS EPB meeting, where the student receives feedback from the BS EPB members. The presentation based on the submitted research project - detailed ISP will contain information about the current issues, introduction to the current state of knowledge, objectives and hypotheses and proposed solutions (methodological approaches, alternative solutions in case the main methodological approaches fail, etc.).

2nd year:

Work on the research project and fulfil study obligations. Completion of the State Doctoral Exam (SDE) is recommended from the middle of the second year onwards.

3rd year:

The student presents the progress of the research project and the current study within the deadline set by the BS EPB (ideally at the beginning of the year) and discusses the further development of the project with the BS EPB.

4th year and higher:

At the beginning of the 4th year (and additional years beyond the 4th year) the student will present the results of their previous work in a presentation where they will emphasize the results of their work, any realized or planned publications, and the outlook for their timely completion of doctoral studies. The presentation should include an estimation for the date of writing and submission of the doctoral dissertation. The student will submit their presentation in PDF form to the BS EPB. BS EPB appeals for the completion of studies and submission of a dissertation for defence by the end of the 4th year of study.

Annual evaluation of the student

At the end of each year (i.e. September, or the date according to SIS) the student adds information about the progress of their studies to the SIS for the past academic year and this is evaluated by their supervisor in SIS. The student must add information about meeting for consultation with both reporters to their annual evaluation. The suggestion of the supervisor is one of the bases for the evaluation by the BS EPB (the evaluation of the supervisor and the BS EPB do not necessarily coincide). Internal correspondents prepare a draft evaluation of the student by the BS EPB; the evaluation should describe the student’s work and results, not talent. The OR will discuss the student’s annual evaluation and the chairman of the BS EPB will summarise the evaluation in a uniform form. According to BS EPB resolution, reasons for a reduced grade (B or C) are in accordance with the following conditions:

  • If the State Doctoral Examination is not passed by the 4th year of study.
  • If, by the end of the 4th year, no article where the student in an author has been published in a peer-reviewed journal with IF.
  • For 4th year students and higher, failure to submit a dissertation for defence when completing publishing activity may also be a reason for a B grade unless there are serious conditions that would make it impossible (severity of reasons will be assessed by the BS EPB during evaluation).


Summary of requirements for EPB doctoral students at Charles University in Prague:

  • Doctoral study is primarily an independent study of a student under the guidance of a supervisor, in which research ends with the presentation of results to the scientific community and the writing of a doctoral dissertation.
  • Part of the doctoral program is participation in specialized lectures and seminars for doctoral students.
  • During the doctoral study, the student must present their work with at least one lecture at an international scientific meeting in English and with at least one poster presentation.
  • The student should complete at least one internship abroad during the study. BS EPB supports student participation in international cooperation.
  • An essential condition for obtaining a PhD degree is publishing see the conditions and types of dissertation. The current requirements of the BS EPB for the publishing activities of doctoral students are listed below - see PhD thesis.
  • Part of the full-time form of study is participation in scientific and pedagogical events at the department. Pedagogical activity, especially within the framework of leading practical exercises provided by DEPB, Fac. Sci., CUNI, is welcome and desirable to a reasonable extent, but not mandatory. Students agree on possible involvement in teaching with the head of the department or guarantors of practical exercises.
  • During the study, the student presents the progress of a scientific project to the members of the BS EPB and the Department of the EPB of the Faculty of Science, Charles University. Regular presentations are usually at the beginning of the 1st year (usually January-March) and the beginning of the 3rd, 4th and each subsequent year (November). Students can also present their progress at the OR meeting based on their request if they want to consult their results with the OR.
  • Successful completion of the State Doctoral Exam by the end of the 4th year of study.
  • Preparation and defence of Phd thesis, if possible, by the end of the 4th year of study.

 

State doctoral exam (SDZ)

The State Doctoral Examination is to be taken by the end of the 4th year of PGS at the latest. The condition for holding the State Doctoral Examination is the completion of study obligations according to an individual study plan. During the State Doctoral Examination, the student demonstrates orientation in the field and expert orientation within the topic of the dissertation.

Thematic areas for the SDZ are:

The goal of the exam in the 2 mandatory subject areas is for the student to show a broad theoretical foundation in the field – the student should show good orientation, without excessive details, in topics in the field of plant biology that are not necessarily connected to their dissertation work. If the dissertation is focused on physiological, anatomical or ecophysiological topics, a deeper knowledge of Plant Anatomy and Physiology will be expected. If the dissertation is devoted to cellular or molecular issues, more detailed knowledge in the subject Cellular and Molecular Biology of Plants will be expected.

Elective subjects (usually from the list of courses taught at the Faculty of Science) are approved by the OR based on a student's proposal (decided with their supervisor). It is recommended that the student first consults with the chairperson of the OR before applying SDZ. Elective courses correspond in their specialization to the specialization of the topic of the dissertation. The requirement for fulfilment is a deeper knowledge of the area and the ability to interpret them in a broader context. However, the content of the questions takes into account the student's focus and in topics close to the content of his dissertation, the student is expected to have detailed and up-to-date, i.e. expert knowledge that may go beyond the subjects taught.

If a student does not attend the State Doctoral Examination for serious reasons within the period for which they are registered, they will apologize in writing for their absence as soon as possible. The Dean decides on the regularity of the apology. Apologies from the term of the SDE or the defence are governed by the rules for the organization of study at the Faculty of Science. If the examination cannot be held for relevant reasons (i.e. student's illness, the committee is not able to pass a resolution), the chairman of the committee will propose the nearest possible alternative date of the examination in agreement with the student.

The student may take the State Doctoral Examination no more than twice (Each student is entitled to a second chance). If the student does not take the State Doctoral Exam even in the corrective term, he/she did not meet the requirement set out by the Study and Examination Regulations of Charles University and their studies will be ended.

 

Dissertation (PhD thesis)

Requirements of the BS EPB on the publishing activity of doctoral candidates and recommendation regarding the structure of the submitted doctoral dissertation thesis (DDT) for defence within the field of plant anatomy and physiology, Faculty of Science, Charles University in Prague:

DDT can be written in one of two forms: classic and abbreviated. The condition for defending the dissertation is a verifiable publication activity of the student. Requirements for publishing activities depend on the chosen form of work:

  1. Dissertation in the classical form of a comprehensive manuscript (or scientific monography) must be accompanied by at least one manuscript on the theme of the dissertation work published or accepted in a journal with IF where the student is the first author. In such a case, members of the defence committee and opponents of the thesis will assess whether the thesis contains a sufficient number of suitably designed, high-quality, experiments and relevant discussion for the obtained results.
  2. Dissertation in an abbreviated form as the collection of at least 3 scientific works, with accompanying commentary, which includes both - a thorough, deep discussion of the results in the context of current knowledge and determining of open problems for future research. Articles in journals with IF or chapters in monographs related to the topic of the doctoral project are considered scientific works. These publications must be published or accepted for publication, at least two of which must be the first author of the doctoral student and at least two of these publications are original scientific works. At least one original work, where the student is the first author, must be published in a journal with IF ≥ 1.5 (approximately the median of the field). In the case of a significant publication with IF ≥ 4 (approximately the upper decile of the field), where the doctoral student is the first author, it is possible to have only a total of 2 publications sent or received and a third or another in the form of a manuscript ready for submission.

Deadlines:

  • State doctoral exam must be completed before submitting the dissertation.
  • The defence should take place by the end of the 4th year of study.
  • For students studying in a 4-year program, the maximum length of study is 8 years (for students admitted in 2016 and later).
  • The defences can take place until the end of September in the 8th year of study, otherwise, the study is administratively terminated.
  • Deadlines for defence after the submission of the dissertation are given by EPB OR:
    • For defenses in August - September (exact date not guaranteed) the deadline is May 30th
    • For defenses in September - October (exact date not guaranteed) the deadline is June 30th
    • For defenses in October - November (exact date not guaranteed) the deadline is July 30th

BS EPB asks that students give 1-2 months advance notice of the intended submission date when submitting DDT. The nearest defence date will be determined according to the availability of committee members and opponents.


To clarify the deadlines for submitting the work according to the Rules for the Organization of Study at any given time currently valid at Charles University:

  1. The chairman of the committee, after consultation with the opponents and in cooperation with the Study Department, will ensure that the work is sent to the opponents 4 weeks before the defence proceedings.
  2. The opponent will prepare a report within 4 weeks of its delivery.
  3. The chairman of the commission shall propose a date no later than 4 weeks before the defence.
  4. At least two weeks before the defence, the opponent's opinions will be sent to the members of the committee.


DDT submission: 

Opponents of the DDT:

There are at least 2 opponents, it is not possible to make an exception to this rule. Opponents should be impartial. An opponent cannot be a supervisor, consultant or one of the authors of a publication submitted as part of a dissertation. The opponent has 4 weeks from the receipt of the DDT to prepare the report. The time can be shorter if the student/supervisor agrees with the opponent. 

 

Dissertation defense

The defense is public.


Even in the case where both opponents express positive opinions of the defense, the participation of at least one opponent is expected. Exceptions to this rule can only be made in justified cases. If one or more opponents' opinions are negative, both opponents must be present at the defense. It is not possible to make an exception to this rule. The opponent may be present via teleconference.

The course of the defense:

  1. Introductory speech by the chairman of the committee, introducing the defending doctoral student and getting the audience acquainted with their professional CV and publishing activities.
  2. Supervisor's statement (brief evaluation of the student and their work during the study, including a statement as to whether the supervisor recommends the thesis for the defence. The supervisor‘s statement will be recorded in the defense record. It is recommended to have this speech in writing and read it during the defence. In this case, the supervisor‘s written statement may be submitted to the SIS alongside the defense files.
  3. The dissertation presentation of the defending doctoral student (30 - 40 min.)
  4. Reading of opponents' reports. According to the agreement, it is possible that the student immediately responds to the comments of opponents during the reading of the report.
  5. Defense - reactions/answers of the doctoral student to the questions and comments of the opponents contained in the assessments.
  6. General discussion of the dissertation. Other supplementary questions and comments from members of the commission and others present at the defense.
  7. After the discussion - closed meeting of committee members, opponents, and supervisors, voting of committee members on the outcome of the defense. Ballot papers are used for voting.
  8. Public announcement of the results of the defense.

If the committee determines that the candidate has not successfully defended their dissertation, they should specify if/how the work needs to be changed or supplemented and give their requirements at the same meeting. These requirements shall be decided by the committee by a majority of votes cast.

If a student fails to defend the DDT in the first, proper term, they have another corrective term available, which is permitted by the Dean of the Faculty of Science, Charles University.

If for relevant reasons, the student does not appear for the defense on the day for which they are registered, they will apologize in writing for their absence immediately after resolving the situation The student is obliged to document the facts of their absence. The Dean decides if the apology is proper. The study department shall record the apology or forfeiture in the SIS.

If the defense cannot take place within the set deadline due to serious reasons (e.g. student's illness, the committee cannot come to a decision), the chairman of the commission will propose the nearest possible alternative date of the defense in agreement with the student and opponents.

The student may defend the dissertation no more than twice, i.e. they are entitled to one correction term. If the student does not defend the dissertation even in the corrective term, they have not fulfilled the requirement set by the Study and Examination Regulations of Charles University.

 

Completion or termination of study

  • The day of the proper completion of the doctoral study is the day when the dissertation was defended. It follows from the provisions of the Study and Examination Regulations that the student must pass the State Doctoral Exam and defend the dissertation by the end of the 9th year of study (it is not enough to submit the dissertation by this deadline) - the student will determine the exact date at the Study Department of Charles University.
  • Failure to meet these deadlines leads to the termination of studies for non-compliance with the requirements arising from the study program. It follows from the Rules for the Organization of Studies that the dissertation must be submitted for defence no later than 12 weeks before the expiry of a maximum study period of nine years.
  • If a doctoral student decides to leave studies for any reason, it is necessary to notify the decision of the doctoral study department of the Faculty of Science of Charles University in writing (to the relevant vice-dean with a copy to the branch council - chairman of the BS EPB).