Study requirements for PhD students of Immunology
The goal of study is to train students at advanced level in immunology. The students should acquire broad knowledge of the research area, master their research topic, become competent in conducting and planning experiments, get trained in scientific writing, and obtain qualification which would make them competitive candidates for positions in research, teaching, and technologies internationally.
Learning goal 1
Students must take at least three study obligations (courses) and schedule them within the first 3 years of study. When preparing their proposal of the individual study plan (ISP) for approval by the Subject area board (Board) in the Study Information System of the Charles University (SIS), students should include all three courses in the plan.
All students must take the obligatory “Grant application strategy and preparation of scientific publication” course. After the theoretical background is explained in several lectures, the student will prepare a grant application related to the Ph.D. project in English, using the forms and guidelines of the Grant Agency of the Czech Republic.
Students choose at least two study obligations from the list below. Students should actively seek the opinion of their mentors about the suitability of courses with respect to their project. The prerequisite for the inclusion of courses is that students have not passed them in previous or concurrent study programs.
- Protein dynamics in development and cancer
- Innate immunity
- Advances in Immunology 1
- Immunology - a practical course
- Clinical Cases in Immunology
- Immunology - a systems biology view
- Animal models in immunology
- Evolutionary and ecological immunology
- Molecular mechanisms of immune evolution
- Regulation mechanisms of immunity (*)
- Viruses and host immune systém (*)
- Molecular Biology of Cancer I (*)
- Molecular Biology of Cancer II
- Fluorescent microscopy in cell biology
- Advances in molecular biology and genetics (Institute of Molecular Genetics of the ASCR, v. v. i.) https://pokroky.img.cas.cz/ (according to the information for the current academic year)
(*) enquire about the availability of the course in English
• Processing and analysis of microscopic image in biomedicine (Institute of Molecular Genetics of the ASCR, v. v. i.) https://www.img.cas.cz/2016/04/26119-zpracovani-a-analyza-mikroskopickych-obrazu-v-biomedicine/ (according to the information for the current academic year)
• Microscopic methods in biomedicine (Institute of Molecular Genetics of the ASCR, v. v. i.) https://www.img.cas.cz/2013/06/15613-mikroskopicke-metody-v-biomedicine/ (according to the information for the current academic year)
• Transmission electron microscopy in life sciences (Institute of Molecular Genetics of the ASCR, v. v. i.) https://www.img.cas.cz/2015/02/21825-transmission-electron-microscopy-in-life-sciences/ (according to the information for the current academic year)
• MB140C75E Fluorescence spectroscopy in biology
Learning goal 2
Internships and visits in cooperating laboratories
Students conduct part of their work or training at foreign institution for a total length of at least one month or directly participate in other forms of international cooperation, such as participation in an international creative project with results published or presented abroad. The recommended form is an internship (in total for at least three months) with emphasis on advanced methods or new approaches/ models.
Presentations of results
Students are required to attend the conference of doctoral students, which is summoned every year by the Board. Students actively participate in its organization. During the conference, students present results of their projects and discuss methods and issues of common interest. Both the Board members and the mentors are invited to the conference.
Active participation in international conferences according to the focus and possibilities of the mentor’s team is also recommended.
The state doctoral exam is an important control point of the study, in addition to the annual ISP checks. The exam serves to test student’s understanding of the research project and his/ her orientation in the research field. The committee assesses depth and breadth of knowledge of developmental and cell biology with emphasis on areas related to the project. The recommended timing of the exam is the second semester of the second year of study or the first semester of the third year, so that the exam can serve as a useful feedback for the student. Postponing the exam after the 3rd year without reason may affect student’s grading during the subsequent annual evaluation.
The applicant must be an author/ co-author of at least two papers accepted in peer-reviewed journals indexed in the Web of Science (preferably with IF above the research field median) and should be a first author on at least one publication (shared first authorship should be communicated ex ante with the Board). In exceptional and warranted cases, the Board may decide otherwise; an example of such situation may be one excellent first author publication.
The thesis should be written as concise, fair and comprehensive information about the applicant's scientific achievements. It should enable the reviewers and the defense committee to assess whether the candidate has acquired both theoretical knowledge and methodical experience as prerequisite for independent scientific work in the field. The candidate should address the scientific problems and open questions of the project and formulate his/ her independent opinions.
a) Abstract – It should summarize the project’s aims and results for the public; it should not exceed 500 words.
b) Introduction – It should be outlined as brief review of current knowledge related to the project. Recommended length is ca 20 pages of standard manuscript formatting.
c) Methods, Results – These sections should describe in detail the methods and the results of experiments carried out by the applicant, which have not become part of the published papers/ submitted manuscripts. The published papers/ submitted manuscripts should be included as supplements.
d) Discussion – This section gives the author the opportunity to present her/ his independent opinions on the results and their significance. It should reflect the level of knowledge at the date of thesis submission and it should mention relevant literature containing supportive or contradictory results. Minimum length is 10 pages.
e) Summary - Summary of the main results. Recommended length is 1 page.
f) Accompanying sections - list of abbreviations, list of references, information on data repositories or websites where appropriate, statement describing the contribution of the applicant to the published work, including a detailed statement about his/ her role in the preparation of the publications.
g) Publications and submitted manuscripts which contain the results obtained by the student.
The text in parts a) to e) should be written by the student and must not be contained elsewhere. The text cannot be copied, even in part, from the publications in section g) or other texts. The text can be written in English, Czech or Slovak. Formatting of the text, figures, tables and accompanying data should comply with the rules for manuscript submission of a journal of choice, such as the journal where one of the author’s papers was published.